diff --git a/doc/source/whats_new.rst b/doc/source/whats_new.rst
index 5ff2f77d1..3c7c0a5fd 100644
--- a/doc/source/whats_new.rst
+++ b/doc/source/whats_new.rst
@@ -14,6 +14,8 @@ BUG
 
     - Fix ``mne.io.add_reference_channels`` not setting ``info[nchan]`` correctly by `Federico Raimondo`_
 
+    - Fix ``mne.stats.bonferroni_correction`` reject mask output to use corrected p-values by `Denis Engemann`_
+
 .. _changes_0_9:
 
 Changelog
diff --git a/mne/stats/multi_comp.py b/mne/stats/multi_comp.py
index 51751ea1a..a26b4a772 100644
--- a/mne/stats/multi_comp.py
+++ b/mne/stats/multi_comp.py
@@ -98,5 +98,5 @@ def bonferroni_correction(pval, alpha=0.05):
     """
     pval = np.asarray(pval)
     pval_corrected = pval * float(pval.size)
-    reject = pval < alpha
+    reject = pval_corrected < alpha
     return reject, pval_corrected

BUG/API issue with multi_comp.bonferroni_correction
Do people agree that this is a bug, at least a very unexpected output:
https://github.com/mne-tools/mne-python/blob/master/mne/stats/multi_comp.py#L101

`pval_corrected` should instead be used for creating the output mask.

@agramfort @Eric89GXL @mainakjas 
diff --git a/mne/stats/tests/test_multi_comp.py b/mne/stats/tests/test_multi_comp.py
index 4cba14113..76b2c99db 100644
--- a/mne/stats/tests/test_multi_comp.py
+++ b/mne/stats/tests/test_multi_comp.py
@@ -1,5 +1,6 @@
 import numpy as np
-from numpy.testing import assert_almost_equal, assert_allclose, assert_raises
+from numpy.testing import (
+    assert_almost_equal, assert_allclose, assert_raises, assert_array_equal)
 from nose.tools import assert_true
 from scipy import stats
 
@@ -25,6 +26,8 @@ def test_multi_pval_correction():
     assert_true(pval_bonferroni.ndim == 2)
     assert_true(reject_bonferroni.ndim == 2)
     assert_allclose(pval_bonferroni / 10000, pval)
+    reject_expected = pval_bonferroni < alpha
+    assert_array_equal(reject_bonferroni, reject_expected)
 
     fwer = np.mean(reject_bonferroni)
     assert_almost_equal(fwer, alpha, 1)

pip install -e .[dev]
parse_log_pytest
requirements.txt
numpy>=1.16.0 pandas>=1.0.0 scikit-learn h5py pysurfer nose nose-timer pytest
apt-get update apt-get install -y gcc
3.7
requirements/base.txt
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
apptools==5.2.1
certifi @ file:///croot/certifi_1671487769961/work/certifi
configobj==5.0.9
cycler==0.11.0
envisage==7.0.3
exceptiongroup==1.2.2
fonttools==4.38.0
h5py==3.8.0
importlib-metadata==6.7.0
importlib-resources==5.12.0
iniconfig==2.0.0
joblib==1.3.2
kiwisolver==1.4.5
matplotlib==3.5.3
mayavi==4.8.1
-e git+https://github.com/mne-tools/mne-python.git@b143c6df244dca2e6121048fae99cb6e1cfa84ab#egg=mne
nibabel==4.0.2
nose==1.3.7
nose-timer==1.0.1
numpy==1.21.6
packaging==24.0
pandas==1.3.5
Pillow==9.5.0
pluggy==1.2.0
pyface==8.0.0
Pygments==2.17.2
pyparsing==3.1.4
pysurfer==0.11.2
pytest==7.4.4
python-dateutil==2.9.0.post0
pytz==2025.2
scikit-learn==1.0.2
scipy==1.7.3
six==1.17.0
threadpoolctl==3.1.0
tomli==2.0.1
traits==6.4.3
traitsui==8.0.0
typing_extensions==4.7.1
vtk==9.3.1
zipp==3.15.0

name: mne-python
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - ca-certificates=2025.2.25=h06a4308_0
  - certifi=2022.12.7=py37h06a4308_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.4.4=h6a678d5_1
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - ncurses=6.4=h6a678d5_0
  - openssl=1.1.1w=h7f8727e_0
  - pip=22.3.1=py37h06a4308_0
  - python=3.7.16=h7a1cb2a_0
  - readline=8.2=h5eee18b_0
  - setuptools=65.6.3=py37h06a4308_0
  - sqlite=3.45.3=h5eee18b_0
  - tk=8.6.14=h39e8969_0
  - wheel=0.38.4=py37h06a4308_0
  - xz=5.6.4=h5eee18b_1
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - apptools==5.2.1
      - configobj==5.0.9
      - cycler==0.11.0
      - envisage==7.0.3
      - exceptiongroup==1.2.2
      - fonttools==4.38.0
      - h5py==3.8.0
      - importlib-metadata==6.7.0
      - importlib-resources==5.12.0
      - iniconfig==2.0.0
      - joblib==1.3.2
      - kiwisolver==1.4.5
      - matplotlib==3.5.3
      - mayavi==4.8.1
      - nibabel==4.0.2
      - nose==1.3.7
      - nose-timer==1.0.1
      - numpy==1.21.6
      - packaging==24.0
      - pandas==1.3.5
      - pillow==9.5.0
      - pluggy==1.2.0
      - pyface==8.0.0
      - pygments==2.17.2
      - pyparsing==3.1.4
      - pysurfer==0.11.2
      - pytest==7.4.4
      - python-dateutil==2.9.0.post0
      - pytz==2025.2
      - scikit-learn==1.0.2
      - scipy==1.7.3
      - six==1.17.0
      - threadpoolctl==3.1.0
      - tomli==2.0.1
      - traits==6.4.3
      - traitsui==8.0.0
      - typing-extensions==4.7.1
      - vtk==9.3.1
      - zipp==3.15.0
prefix: /opt/conda/envs/mne-python

mne/stats/tests/test_multi_comp.py::test_multi_pval_correction
mne/stats/multi_comp.py doc/source/whats_new.rst
mne/stats/multi_comp.py doc/source/whats_new.rst