The atypical C-type protein kinases (aPKCs) comprise the third subclass of the PKC family functionally defined by insensitivity to phorbol esters, diacylgylcerol and calcium. aPKCs have been implicated in numerous biological processes including cell proliferation and survival, cell polarity, migration and inflammation. However, only insufficient data exist with regard to aPKC isoform specificity, since both mammalian aPKCs, PKC iota/lambda and PKC zeta, exhibit a high structural homology and very similar biochemical properties. In this study, we therefore used isoform-specific riboprobes and antibodies to define the characteristic expression profile of each aPKC isoform during mouse embryogenesis. Both, PKC iota/lambda and zeta show highly specific temporal and spatial patterns of expression which may help in distinguishing physiological functions of these isoforms.