Neurons of the cochlear nucleus (CN) receive extrinsic and intrinsic cholinergic inputs, the effects of which appear to be mediated primarily by muscarinic acetylcholine receptors (mAChRs). To investigate the distribution of mAChRs and the correlation of pre- and post-synaptic cholinergic markers in CN, we used a monoclonal anti-mAChR antibody (M35) and a monoclonal antibody against choline acetyltransferase (ChAT) to perform immunohistochemistry on rat brain sections, and we also carried out histochemistry for acetylcholinesterase (AChE) activity. The density distributions of ChAT immunohistochemistry and AChE activity histochemistry agreed well with previous quantitative measurements of the activity distributions of these enzymes. A generally close correlation between densities of M35 and ChAT immunoreactivities was found across subregions of rat CN. The localizations of M35 and ChAT immunoreactivities suggest that cholinergic synapses are mostly axosomatic in ventral CN and possibly mostly axodendritic in dorsal CN. Prominent differences in density and appearance between M35 immunoreactivity and AChE activity were found in the regions of the rat CN where granule cells predominate.