This study examined the distribution of complement C1qB and C4 mRNAs during rat brain development by northern blot and in situ hybridization. Both C1q and C4 mRNAs were already present at embryonic day 14 (E14) and showed little change in abundance through six weeks postnatal. At E16, C1qB mRNA was present at high abundance in putative microglia/macrophages in cortical marginal and intermediate zones, and hippocampal analge, but not in the neurogenic ventricular or sub-ventricular zones. C4 mRNA had a broadly similar regional distribution, but was present at lower abundance in a larger number of cells, putatively neurons. The distribution pattern for C1qB and C4 mRNAs did not change appreciably as brain development proceeded. The lower prevalence of C mRNAs in neuroepithelial or subventricular zones suggests an inverse relationship of C mRNA to cell proliferation. The frequency of apoptotic nuclear profiles, which was as much as ten-fold higher at P7 vs. E17, did not correlate anatomically with C1qB or C4 mRNA levels. Thus, the widespread distribution and consistent presence of each C mRNA during development argues against a role for C in programmed cell death during brain development. We suggest that C1q and C4 components have novel roles during brain development that may be unrelated to normal cytotoxic actions of the activated classical C cascade.