The protein kinase C (PKC) family of serine/threonine kinases plays a role in a variety of physiological and pathophysiological processes in the brain including development, synaptic plasticity, epilepsy, ischemia, and neuronal cell death. The subgroup of atypical PKCs (aPKCs) comprises of three members, PKCiota/lambda, PKCzeta, and PKMzeta, with high amino acid homology. We used specific RNA probes and in situ hybridization to determine the expression patterns of all the three isoforms in the adult mouse brain. PKCiota and PKMzeta were found to be broadly expressed in most of the cortex, the limbic system, and the thalamus. In contrast, PKCzeta transcription was restricted to distinct forebrain areas and the cerebellum. Here we present a first comprehensive overview of isotype-specific aPKC distribution in the central nervous system, thereby providing a solid ground for further studies on the functional implications of the different aPKCs in the neuronal system.