Calmodulin (CaM), a multifunctional intracellular calcium receptor, is a key element in signaling mechanisms. It is encoded in vertebrates by multiple apparently redundant genes (CaM I, II, III). To investigate whether differential expression takes place in the developing rat brain, a quantitative in situ hybridization analysis was carried out involving 15 brain areas at six ages between embryonic day 19 and postnatal day 20 (PD20) with gene-specific [(35)S]cRNA probes. A widespread, developmental stage-specific and differential expression of the three CaM genes was observed. The characteristic changes in the CaM mRNA levels in the examined time frame allowed the brain regions to be classified into three categories. For the majority of the areas (e.g. the piriform cortex for CaM III), the signal intensities peaked at around PD10 and the expression profile was symmetric (type 1). Other regions (e.g. the cerebral cortex, layer 1 for CaM II) displayed their highest signal intensities at the earliest age measured, followed by a gradual decrease (type 2). The signal intensities in the regions in the third group (e.g. the hypothalamus for CaM III) fluctuated from age to age (type 3). Marked CaM mRNA levels were measured for each transcript corresponding to the three CaM genes in the molecular layers of the cerebral and cerebellar cortici and hippocampus, suggesting their dendritic translocation. The highest signal intensity was measured for CaM II mRNA, followed by those for CaM III and CaM I mRNAs on PD1. However, the CaM II and CaM III mRNAs subsequently decreased steeply, while the CaM I mRNAs were readily detected even on PD20. Our results suggest that during development (1) the transcription of the CaM genes is under differential, area-specific control, and (2) a large population of CaM mRNAs is targeted to the dendritic compartment in a gene-specific manner.