The cytoarchitecture of the cerebral cortex in mammals has been traditionally investigated using Nissl, Golgi, or myelin stains and there are few comparative studies on the relationships between neuronal morphology and neurochemical specialization. Most available studies on neuronal subtypes identified by their molecular and morphologic characteristics have been performed in species commonly used in laboratory research such as the rat, mouse, cat, and macaque monkey, as well as in autopsic human brain specimens. A number of cellular markers, such as neurotransmitters, structural proteins, and calcium-buffering proteins, display a highly specific distribution in distinct classes of neocortical neurons in a large number of mammalian species. In this article, we present an overview of the morphologic characteristics and distribution of three calcium-binding proteins, parvalbumin, calbindin, and calretinin, and of a component of the neuronal cytoskeleton, nonphosphorylated neurofilament protein in the neocortex of various species, representative of the major subdivisions of mammals. The distribution of these neurochemical markers defined several species- and order-specific patterns that permit assessment of the degree to which neuronal morphomolecular specialization, as well as the regional and laminar distribution of distinct cell types in the neocortex, represents derived or ancestral features. In spite of the remarkable diversity in morphologic and cellular organization that occurred during mammalian neocortical evolution, such patterns identified several associations among taxa that closely match their phylogenetic relationships. © 2005 Wiley-Liss, Inc.