The cDNA for the mouse bone morphogenetic protein type II receptor (BMPR-II) was isolated using the human counterpart as a probe and its genomic structure was determined. The cDNA encodes a protein of 1,038 amino acids with a single transmembrane domain, a serine/threonine kinase domain, and a long carboxy-terminal tail. The overall amino acid sequence identity between the mouse and the human BMPR-II is 96.6%. mRNA is widely distributed in various adult tissues. The gene is encoded by 13 exons spanning over 80 kb. Two large introns (intron 1 and 3) contribute to the majority of the gene size, as in the mouse activin type II receptor gene. The intron/exon boundaries were sequenced. The results suggest that alternative splicing can yield a shorter form of BMPR-II of 530 amino acids, as reported previously. Knowledge of the structure of the BMPR-II gene is essential for the understanding of the role of bone morphogenetic proteins in the developmental and physiological processes of animals.