C57BL/6 and DBA/2 mice present a number of behavioral and neurobiological differences and react in opposite ways to cholinergic drugs. A morphological study during ontogony of brain cholinergic organization of these strains was therefore performed by using acetylcholinesterase pharmacohistochemistry and choline acetyltransferase immunohistochemistry. Cross-sectional areas and rostrocaudal measures of selected brain regions were analyzed. C57 mice were characterized by a lower cholinergic density. This deficit was most pronounced in the striatum, the nucleus basalis of Meynert and the nucleus of the diagonal band of Broca. The observed strain differences were shown to be age-related by using mice aged 20–110 postnatal days. The differentially expressed cholinergic deficit in C57 mice may lead to an approach of the degenerative patterns of cholinergic systems in humans.