diff --git a/fmriprep/data/reports-spec-func.yml b/fmriprep/data/reports-spec-func.yml
index 04acea2c..cf932014 100644
--- a/fmriprep/data/reports-spec-func.yml
+++ b/fmriprep/data/reports-spec-func.yml
@@ -104,6 +104,21 @@ sections:
       anatomical white matter mask, which appears as a red contour.
     static: false
     subtitle: Alignment of functional and anatomical MRI data (coregistration)
+  - button:
+      type: button
+      class: btn btn-primary
+      data-toggle: collapse
+      data-target: '#flippedcoreg'
+      text: 'Alignment of functional and flipped anatomical MRI data'
+  - div:
+      class: collapse
+      id: 'flippedcoreg'
+      reportlets:
+      - bids: {datatype: figures, desc: flippedcoreg, suffix: bold}
+        caption: This panel shows the alignment of the reference EPI (BOLD) image to the
+          left-right flipped anatomical (T1-weighted) image.
+        static: false
+        subtitle: Left-right flip check, alignment of functional and flipped anatomical MRI data
   - bids: {datatype: figures, desc: rois, suffix: bold}
     caption: Brain mask calculated on the BOLD signal (red contour), along with the
       regions of interest (ROIs) used for the estimation of physiological and movement
diff --git a/fmriprep/data/reports-spec.yml b/fmriprep/data/reports-spec.yml
index 4ec02bda..17bc8caf 100644
--- a/fmriprep/data/reports-spec.yml
+++ b/fmriprep/data/reports-spec.yml
@@ -130,6 +130,21 @@ sections:
       anatomical white matter mask, which appears as a red contour.
     static: false
     subtitle: Alignment of functional and anatomical MRI data (coregistration)
+  - button:
+      type: button
+      class: btn btn-primary
+      data-toggle: collapse
+      data-target: '#flippedcoreg'
+      text: 'Alignment of functional and flipped anatomical MRI data'
+  - div:
+      class: collapse
+      id: 'flippedcoreg'
+      reportlets:
+      - bids: {datatype: figures, desc: flippedcoreg, suffix: bold}
+        caption: This panel shows the alignment of the reference EPI (BOLD) image to the
+          left-right flipped anatomical (T1-weighted) image.
+        static: false
+        subtitle: Left-right flip check, alignment of functional and flipped anatomical MRI data
   - bids: {datatype: figures, desc: rois, suffix: bold}
     caption: Brain mask calculated on the BOLD signal (red contour), along with the
       regions of interest (ROIs) used for the estimation of physiological and movement
diff --git a/fmriprep/interfaces/reports.py b/fmriprep/interfaces/reports.py
index 8f26c374..76d91a36 100644
--- a/fmriprep/interfaces/reports.py
+++ b/fmriprep/interfaces/reports.py
@@ -67,6 +67,17 @@
 \t\t\t<li>Slice timing correction: {stc}</li>
 \t\t\t<li>Susceptibility distortion correction: {sdc}</li>
 \t\t\t<li>Registration: {registration}</li>
+\t\t\t<li>Left-right flip check warning: {lr_flip_warning}</li>
+\t\t<table>
+\t\t\t<tr>
+\t\t\t\t<th>Original Registration Cost</th>
+\t\t\t\t<th>Flipped Registration Cost</th>
+\t\t\t</tr>
+\t\t\t<tr>
+\t\t\t\t<td>{cost_original}</td>
+\t\t\t\t<td>{cost_flipped}</td>
+\t\t\t</tr>
+\t\t</table>
 \t\t\t<li>Non-steady-state volumes: {dummy_scan_desc}</li>
 \t\t</ul>
 \t\t</details>
@@ -218,6 +229,12 @@ class FunctionalSummaryInputSpec(TraitedSpec):
         desc='Whether to initialize registration with the "header"'
         ' or by centering the volumes ("t1w" or "t2w")',
     )
+    flip_info = traits.Dict(
+        traits.Enum('lr_flip_warning', 'cost_original', 'cost_flipped'),
+        traits.Either(traits.Bool(), traits.Float()),
+        desc='Left-right flip check warning and registration costs',
+        mandatory=True,
+    )
     tr = traits.Float(desc='Repetition time', mandatory=True)
     dummy_scans = traits.Either(traits.Int(), None, desc='number of dummy scans specified by user')
     algo_dummy_scans = traits.Int(desc='number of dummy scans determined by algorithm')
@@ -279,6 +296,12 @@ def _generate_segment(self):
         if n_echos > 2:
             multiecho = f'Multi-echo EPI sequence: {n_echos} echoes.'
 
+        lr_flip_warning = (
+            '<span style="color:red;">LR flip detected</span>'
+            if self.inputs.flip_info.get('lr_flip_warning', False)
+            else 'none'
+        )
+
         return FUNCTIONAL_TEMPLATE.format(
             pedir=pedir,
             stc=stc,
@@ -288,6 +311,9 @@ def _generate_segment(self):
             dummy_scan_desc=dummy_scan_msg,
             multiecho=multiecho,
             ornt=self.inputs.orientation,
+            lr_flip_warning=lr_flip_warning,
+            cost_original=self.input.flip_info.get('cost_original', None),
+            cost_flipped=self.input.flip_info.get('cost_flipped', None),
         )
 
 
@@ -369,3 +395,40 @@ def get_world_pedir(ornt, pe_direction):
         f'Orientation: {ornt}; PE dir: {pe_direction}'
     )
     return 'Could not be determined - assuming Anterior-Posterior'
+
+
+class _CheckFlipInputSpec(BaseInterfaceInputSpec):
+    cost_original = File(
+        exists=True,
+        mandatory=True,
+        desc='cost associated with registration of BOLD to original T1w images',
+    )
+    cost_flipped = File(
+        exists=True,
+        mandatory=True,
+        desc='cost associated with registration of BOLD to the flipped T1w images',
+    )
+
+
+class _CheckFlipOutputSpec(TraitedSpec):
+    flip_info = traits.Dict(
+        traits.Enum('warning', 'cost_original', 'cost_flipped'),
+        traits.Either(traits.Bool(), traits.Float()),
+        desc='Left-right flip check warning and registration costs',
+        mandatory=True,
+    )
+
+
+class CheckFlip(SimpleInterface):
+    """Check for a LR flip by comparing registration cost functions."""
+
+    input_spec = _CheckFlipInputSpec
+    output_spec = _CheckFlipOutputSpec
+
+    def _run_interface(self, runtime):
+        self._results['flip_info'] = {
+            'warning': self.inputs.cost_flipped < self.inputs.cost_original,
+            'cost_original': self.inputs.cost_original,
+            'cost_flipped': self.inputs.cost_flipped,
+        }
+        return runtime
diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index f66d49eb..3161c332 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -289,6 +289,9 @@ def init_bold_fit_wf(
                 'boldref2fmap_xfm',
                 'movpar_file',
                 'rmsd_file',
+                # LR flip check
+                'fboldref2anat_xfm',
+                'flipped_boldref',
             ],
         ),
         name='outputnode',
@@ -373,6 +376,8 @@ def init_bold_fit_wf(
             ('coreg_boldref', 'inputnode.coreg_boldref'),
             ('bold_mask', 'inputnode.bold_mask'),
             ('boldref2anat_xfm', 'inputnode.boldref2anat_xfm'),
+            ('fboldref2anat_xfm', 'inputnode.fboldref2anat_xfm'),
+            ('flipped_boldref', 'inputnode.flipped_boldref'),
         ]),
         (summary, func_fit_reports_wf, [('out_report', 'inputnode.summary_report')]),
     ])
@@ -632,7 +637,11 @@ def init_bold_fit_wf(
             (regref_buffer, ds_boldreg_wf, [('boldref', 'inputnode.source_files')]),
             (bold_reg_wf, ds_boldreg_wf, [('outputnode.itk_bold_to_t1', 'inputnode.xform')]),
             (ds_boldreg_wf, outputnode, [('outputnode.xform', 'boldref2anat_xfm')]),
-            (bold_reg_wf, summary, [('outputnode.fallback', 'fallback')]),
+            (bold_reg_wf, outputnode, [
+                ('outputnode.itk_fbold_to_t1', 'fboldref2anat_xfm'), 
+                ('outputnode.flipped_boldref', 'flipped_boldref')]),
+            (bold_reg_wf, summary, [('outputnode.fallback', 'fallback'),
+                                    ('outputnode.flip_info', 'flip_info')]),
         ])
         # fmt:on
     else:
diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
index 4f3450b1..17f1e0db 100644
--- a/fmriprep/workflows/bold/outputs.py
+++ b/fmriprep/workflows/bold/outputs.py
@@ -203,6 +203,9 @@ def init_func_fit_reports_wf(
         't1w_dseg',
         'fieldmap',
         'fmap_ref',
+        # LR flip check
+        'fboldref2anat_xfm',
+        'flipped_boldref',
         # May be missing
         'subject_id',
         'subjects_dir',
@@ -267,6 +270,29 @@ def init_func_fit_reports_wf(
         mem_gb=1,
     )
 
+    # LR flip check
+    t1w_flipped_boldref = pe.Node(
+        ApplyTransforms(
+            dimension=3,
+            default_value=0,
+            float=True,
+            invert_transform_flags=[True],
+            interpolation='LanczosWindowedSinc',
+        ),
+        name='t1w_flipped_boldref',
+        mem_gb=1,
+    )
+    flipped_boldref_wm = pe.Node(
+        ApplyTransforms(
+            dimension=3,
+            default_value=0,
+            invert_transform_flags=[True],
+            interpolation='NearestNeighbor',
+        ),
+        name='boldref_wm',
+        mem_gb=1,
+    )
+
     # fmt:off
     workflow.connect([
         (inputnode, ds_summary, [
@@ -288,6 +314,18 @@ def init_func_fit_reports_wf(
             ('boldref2anat_xfm', 'transforms'),
         ]),
         (t1w_wm, boldref_wm, [('out', 'input_image')]),
+        # LR flip check
+        (inputnode, t1w_flipped_boldref, [
+            ('t1w_preproc', 'input_image'),
+            ('flipped_boldref', 'reference_image'),
+            ('fboldref2anat_xfm', 'transforms'),
+        ]),
+        (inputnode, flipped_boldref_wm, [
+            ('flipped_boldref', 'reference_image'),
+            ('fboldref2anat_xfm', 'transforms'),
+        ]),
+        (t1w_wm, flipped_boldref_wm, [('out', 'input_image')]),
+
     ])
     # fmt:on
 
@@ -409,6 +447,27 @@ def init_func_fit_reports_wf(
         name='ds_epi_t1_report',
     )
 
+    flipped_epi_t1_report = pe.Node(
+        SimpleBeforeAfter(
+            before_label='T1w',
+            after_label='EPI',
+            dismiss_affine=True,
+        ),
+        name='flipped_epi_t1_report',
+        mem_gb=0.1,
+    )
+
+    ds_flipped_epi_t1_report = pe.Node(
+        DerivativesDataSink(
+            base_directory=output_dir,
+            desc='flippedcoreg',
+            suffix='bold',
+            datatype='figures',
+            dismiss_entities=dismiss_echo(),
+        ),
+        name='ds_flipped_epi_t1_report',
+    )
+
     # fmt:off
     workflow.connect([
         (inputnode, epi_t1_report, [('coreg_boldref', 'after')]),
@@ -416,6 +475,11 @@ def init_func_fit_reports_wf(
         (boldref_wm, epi_t1_report, [('output_image', 'wm_seg')]),
         (inputnode, ds_epi_t1_report, [('source_file', 'source_file')]),
         (epi_t1_report, ds_epi_t1_report, [('out_report', 'in_file')]),
+        (inputnode, flipped_epi_t1_report, [('flipped_boldref', 'after')]),
+        (t1w_flipped_boldref, flipped_epi_t1_report, [('output_image', 'before')]),
+        (flipped_boldref_wm, flipped_epi_t1_report, [('output_image', 'wm_seg')]),
+        (inputnode, ds_flipped_epi_t1_report, [('source_file', 'source_file')]),
+        (flipped_epi_t1_report, ds_flipped_epi_t1_report, [('out_report', 'in_file')]),
     ])
     # fmt:on
 
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index 3f7b5e1d..a53070ce 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -127,6 +127,8 @@ def init_bold_reg_wf(
         Affine transform from T1 space to BOLD space (ITK format)
     fallback
         Boolean indicating whether BBR was rejected (mri_coreg registration returned)
+    flip_info
+        Information regarding whether a left-right flip was detected
 
     See Also
     --------
@@ -153,7 +155,16 @@ def init_bold_reg_wf(
     )
 
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=['itk_bold_to_t1', 'itk_t1_to_bold', 'fallback']),
+        niu.IdentityInterface(
+            fields=[
+                'itk_bold_to_t1',
+                'itk_t1_to_bold',
+                'fallback',
+                'flip_info',
+                'itk_fbold_to_t1',
+                'flipped_boldref',
+            ]
+        ),
         name='outputnode',
     )
 
@@ -187,6 +198,9 @@ def init_bold_reg_wf(
             ('outputnode.itk_bold_to_t1', 'itk_bold_to_t1'),
             ('outputnode.itk_t1_to_bold', 'itk_t1_to_bold'),
             ('outputnode.fallback', 'fallback'),
+            ('outputnode.flip_info', 'flip_info'),
+            ('outputnode.itk_fbold_to_t1', 'itk_fbold_to_t1'),
+            ('outputnode.flipped_boldref', 'flipped_boldref'),
         ]),
     ])  # fmt:skip
 
@@ -267,13 +281,16 @@ def init_bbreg_wf(
         Affine transform from T1 space to BOLD space (ITK format)
     fallback
         Boolean indicating whether BBR was rejected (mri_coreg registration returned)
+    flip_info
+        Information regarding whether a left-right flip was detected
 
     """
     from nipype.interfaces.freesurfer import BBRegister
     from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-    from niworkflows.interfaces.nitransforms import ConcatenateXFMs
+    from niworkflows.interfaces.morphology import AxisFlip
 
     from fmriprep.interfaces.patches import FreeSurferSource, MRICoreg
+    from fmriprep.interfaces.reports import CheckFlip
 
     workflow = Workflow(name=name)
     workflow.__desc__ = """\
@@ -308,7 +325,16 @@ def init_bbreg_wf(
         name='inputnode',
     )
     outputnode = pe.Node(
-        niu.IdentityInterface(['itk_bold_to_t1', 'itk_t1_to_bold', 'fallback']),
+        niu.IdentityInterface(
+            [
+                'itk_bold_to_t1',
+                'itk_t1_to_bold',
+                'fallback',
+                'flip_info',
+                'itk_fbold_to_t1',
+                'flipped_boldref',
+            ]
+        ),
         name='outputnode',
     )
 
@@ -347,24 +373,23 @@ def init_bbreg_wf(
     if bold2anat_init == 'header':
         bbregister.inputs.init = 'header'
 
-    transforms = pe.Node(niu.Merge(2), run_without_submitting=True, name='transforms')
-    # In cases where Merge(2) only has `in1` or `in2` defined
-    # output list will just contain a single element
-    select_transform = pe.Node(
-        niu.Select(index=0), run_without_submitting=True, name='select_transform'
+    lr_flip = pe.Node(AxisFlip(axis=0), name='flip')
+    bbregister_flipped = pe.Node(
+        BBRegister(
+            dof=bold2anat_dof,
+            contrast_type='t2',
+            out_lta_file=True,
+        ),
+        name='bbregister',
+        mem_gb=12,
     )
-    merge_ltas = pe.Node(niu.Merge(2), name='merge_ltas', run_without_submitting=True)
-    concat_xfm = pe.Node(ConcatenateXFMs(inverse=True), name='concat_xfm')
+    if bold2anat_init == 'header':
+        bbregister_flipped.inputs.init = 'header'
 
-    workflow.connect([
-        (inputnode, merge_ltas, [('fsnative2t1w_xfm', 'in2')]),
-        # Wire up the co-registration alternatives
-        (transforms, select_transform, [('out', 'inlist')]),
-        (select_transform, merge_ltas, [('out', 'in1')]),
-        (merge_ltas, concat_xfm, [('out', 'in_xfms')]),
-        (concat_xfm, outputnode, [('out_xfm', 'itk_bold_to_t1')]),
-        (concat_xfm, outputnode, [('out_inv', 'itk_t1_to_bold')]),
-    ])  # fmt:skip
+    check_flip = pe.Node(CheckFlip(), name='check_flip')
+
+    transform_wf = _transform_handling_wf(use_bbr=use_bbr)
+    transform_flipped_wf = _transform_handling_wf(use_bbr=use_bbr)
 
     # Do not initialize with header, use mri_coreg
     if bold2anat_init != 'header':
@@ -372,7 +397,8 @@ def init_bbreg_wf(
             (inputnode, mri_coreg, [('subjects_dir', 'subjects_dir'),
                                     ('subject_id', 'subject_id'),
                                     ('in_file', 'source_file')]),
-            (mri_coreg, transforms, [('out_lta_file', 'in2')]),
+            (mri_coreg, transform_wf, [('out_lta_file', 'inputnode.in2')]),
+            (mri_coreg, transform_flipped_wf, [('out_lta_file', 'inputnode.in2')]),
         ])  # fmt:skip
 
         if use_t2w:
@@ -390,15 +416,86 @@ def init_bbreg_wf(
 
         # Otherwise bbregister will also be used
         workflow.connect(mri_coreg, 'out_lta_file', bbregister, 'init_reg_file')
+        workflow.connect(mri_coreg, 'out_lta_file', bbregister_flipped, 'init_reg_file')
 
     # Use bbregister
     workflow.connect([
         (inputnode, bbregister, [('subjects_dir', 'subjects_dir'),
                                  ('subject_id', 'subject_id'),
                                  ('in_file', 'source_file')]),
-        (bbregister, transforms, [('out_lta_file', 'in1')]),
+        (inputnode, bbregister_flipped, [('subjects_dir', 'subjects_dir'),
+                                         ('subject_id', 'subject_id')]),
+        (inputnode, lr_flip), [('in_file', 'in_file')],
+        (lr_flip, bbregister_flipped), [('out_file', 'source_file')],
+        (lr_flip, outputnode), [('out_file', 'flipped_boldref')],
+        (bbregister, check_flip), [('min_cost_file', 'cost_original')],
+        (bbregister, transform_wf, [('out_lta_file', 'inputnode.in1')]),
+        (bbregister_flipped, check_flip), [('min_cost_file', 'cost_flipped')],
+        (bbregister_flipped, transform_flipped_wf, [('out_lta_file', 'inputnode.in1')]),
+        (check_flip, outputnode, [('flip_info', 'flip_info')]),
+        (transform_wf, outputnode, [('outputnode.itk_bold_to_t1', 'itk_bold_to_t1'),
+                                    ('outputnode.itk_t1_to_bold', 'itk_t1_to_bold'),
+                                    ('outputnode.fallback', 'fallback')]),
+        (transform_flipped_wf, outputnode, [('outputnode.itk_bold_to_t1', 'itk_fbold_to_t1')]),
     ])  # fmt:skip
 
+    return workflow
+
+
+def _transform_handling_wf(use_bbr: bool, name: str = 'transform_handling_wf'):
+    """
+    Wire up the co-registration alternatives
+
+    Parameters
+    ----------
+    use_bbr : :obj:`bool` or None
+        Enable/disable boundary-based registration refinement.
+        If ``None``, test BBR result for distortion before accepting.
+    """
+    from niworkflows.engine.workflows import LiterateWorkflow as Workflow
+    from niworkflows.interfaces.nitransforms import ConcatenateXFMs
+
+    workflow = Workflow(name=name)
+    inputnode = pe.Node(
+        niu.IdentityInterface(
+            [
+                'in1',
+                'in2',
+            ]
+        ),
+        name='inputnode',
+    )
+    outputnode = pe.Node(
+        niu.IdentityInterface(
+            [
+                'itk_bold_to_t1',
+                'itk_t1_to_bold',
+                'fallback',
+            ]
+        ),
+        name='outputnode',
+    )
+
+    transforms = pe.Node(niu.Merge(2), run_without_submitting=True, name='transforms')
+    # In cases where Merge(2) only has `in1` or `in2` defined
+    # output list will just contain a single element
+    select_transform = pe.Node(
+        niu.Select(index=0), run_without_submitting=True, name='select_transform'
+    )
+    merge_ltas = pe.Node(niu.Merge(2), name='merge_ltas', run_without_submitting=True)
+    concat_xfm = pe.Node(ConcatenateXFMs(inverse=True), name='concat_xfm')
+
+    workflow.connect(
+        [
+            (inputnode, transforms, [('in1', 'in1'), ('in2', 'in2')]),
+            (transforms, select_transform, [('out', 'inlist')]),
+            (select_transform, merge_ltas, [('out', 'in1')]),
+            (merge_ltas, concat_xfm, [('out', 'in_xfms')]),
+            (concat_xfm, outputnode, [('out_xfm', 'itk_bold_to_t1')]),
+            (concat_xfm, outputnode, [('out_inv', 'itk_t1_to_bold')]),
+        ]
+    )
+
     # Short-circuit workflow building, use boundary-based registration
     if use_bbr is True:
         outputnode.inputs.fallback = False
@@ -531,7 +628,15 @@ def init_fsl_bbr_wf(
         name='inputnode',
     )
     outputnode = pe.Node(
-        niu.IdentityInterface(['itk_bold_to_t1', 'itk_t1_to_bold', 'fallback']),
+        niu.IdentityInterface(
+            [
+                'itk_bold_to_t1',
+                'itk_t1_to_bold',
+                'fallback',
+                'flip_info',
+                'itk_fbold_to_t1',
+            ]
+        ),
         name='outputnode',
     )
 
@@ -576,6 +681,18 @@ def init_fsl_bbr_wf(
         name='fsl2itk_inv',
         mem_gb=DEFAULT_MEMORY_MIN_GB,
     )
+
+    def flip_detection_not_implemented_yet():
+        return {
+            'warning': 'Flip detection not implemented yet for alignment with FSL flirt',
+            'cost_original': '',
+            'cost_flipped': '',
+        }
+
+    check_flip = pe.Node(
+        niu.Function(function=flip_detection_not_implemented_yet, output_names=['flip_info']),
+        name='check_flip',
+    )
     # fmt:off
     workflow.connect([
         (inputnode, mask_t1w_brain, [('t1w_preproc', 'in_file'),
@@ -590,6 +707,7 @@ def init_fsl_bbr_wf(
         (invt_bbr, fsl2itk_inv, [('out_file', 'transform_file')]),
         (fsl2itk_fwd, outputnode, [('itk_transform', 'itk_bold_to_t1')]),
         (fsl2itk_inv, outputnode, [('itk_transform', 'itk_t1_to_bold')]),
+        (check_flip, outputnode, [('flip_info', 'flip_info')]),
     ])
     # fmt:on
 
diff --git a/pyproject.toml b/pyproject.toml
index f707950a..2b3a3235 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ dependencies = [
     "nireports @ git+https://github.com/nipreps/nireports.git@main",
     "nitime",
     "nitransforms >= 21.0.0",
-    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
+    "niworkflows @ git+https://github.com/celprov/niworkflows.git@enh/flip_image",
     "numpy >= 1.22",
     "packaging",
     "pandas",