DOC2A and DOC2B are two homologous genes implicated in synaptic vesicle exocytosis. Their complementary, nonoverlapping expression patterns in adult rat brain suggest that they exert similar functions in different neurons. We have analysed the expression pattern of the two genes in the developing rat brain by in situ hybridization. Unexpectedly, we found no parallel expression of the two genes during development. DOC2B mRNA was highly expressed as early as embryonic day 12 (E12) throughout the neuroepithelium, long before synaptic transmission is functional, and the expression remained abundant from E12 onwards. In contrast, faint expression of DOC2A transcripts was first detected at E17 in ventral brain areas, and it extended gradually to other brain structures in the sequence of their ontology, i.e. structures that had formed first also expressed DOC2A first. At postnatal day 3, both genes were highly expressed throughout the brain. This overlapping expression diverged to the complementary distribution of the adult brain. The temporal and spatial differences in expression point to a functional divergence between these homologous genes during brain development: the pattern of DOC2A is consistent with its proposed synaptic function, whereas that of DOC2B suggests an additional, nonsynaptic role in proliferating cells.