Rat bone morphogenetic protein-3 (BMP-3) cDNA and BMP-3b cDNA were isolated from rat femur cDNA library by the RT-PCR method using degenerate oligonucleotide primers corresponding to human BMP-3. The deduced amino acid sequence of rat BMP-3 in the mature region reveals 2 amino acid changes compared to that of human BMP-3 (98% identity). The deduced BMP-3b amino acid sequence shows 81% similarity with the mature region of rat BMP-3 and only 37% similarity with the propeptide region. By Northern blot analysis, rat BMP-3b mRNA was detected in costa, costicartilage, femur, calvaria, trachea, aorta and brain. Among these tissues, BMP-3b transcripts were predominantly expressed in cerebellum. BMP-3 mRNA was found in femur, calvaria, trachea, lung and ovary. Although BMP-3b and BMP-3 are very closely related to each other, their transcripts are distributed in different tissues except that both are found in bone. The distribution pattern of BMP-3b mRNA suggests that BMP-3b plays an important role in the central nervous system as well as in bone formation and remodeling.