Autoradiography helps to determine the distribution and density of muscarinic receptor (MR) binding sites in the brain. However, it relies on the selectivity of radioligands toward their target. 3H-Pirenzepine is commonly believed to label predominantly M 1MR, 3H-AFDX-384 is considered as M 2MR selective ligand. Here we performed series of autoradiographies with 3H-AFDX-384 (2 nM), and 3H-pirenzepine (5 nM) in WT, M 1KO, M 2KO, and M 4KO mice to address the ligand selectivity. Labeling with 3H-pirenzepine using M 1KO, M 2KO, and M 4KO brain sections showed the high selectivity toward M 1MR. Selectivity of 3H-AFDX-384 toward M 2MR varies among brain regions and depends on individual MR subtype proportion. All binding sites in the medulla oblongata and pons, correspond to M 2MR. In caudate putamen, nucleus accumbens and olfactory tubercle, 77.7, 74.2, and 74.6% of 3H-AFDX-384 binding sites, respectively, are represented by M 4MR and M 2MR constitute only a minor portion. In cortex and hippocampus, 3H-AFDX-384 labels almost similar amounts of M 2MR and M 4MR alongside significant amounts of non-M 2/non-M 4MR. In cortex, the proportion of 3H-AFDX-384 binding sites attributable to M 2MR can be increased by blocking M 4MR with MT3 toxin without affecting non-M 4MR. PD102807, which is considered as a highly selective M 4MR antagonist failed to improve the discrimination of M 2MR. Autoradiography with 3H-QNB showed genotype specific loss of binding sites. In conclusion: while 3H-pirenzepine showed the high selectivity toward M 1MR, 3H-AFDX-384 binding sites represent different populations of MR subtypes in a brain-region-specific manner. This finding has to be taken into account when interpreting the binding data.