We isolated and determined the sequence of cDNA encoding mouse BH-protocadherin (BH-Pcdh) from heart. It encodes a 1069 amino acids (aa) polypeptide exhibiting an overall 97% identity with human BH-Pcdh-a and 83% identity with Xenopus NF-protocadherin. We also determined the alternatively spliced cytoplasmic tail sequence. The cytoplasmic tail of mouse BH-Pcdh-b is short (2 aa) compared with that of human BH-Pcdh-b (14 aa). The cytoplasmic tail of mouse BH-Pcdh-c showed 100% aa identity with that of human BH-Pcdh-c except for a 8-amino-acid insertion. Northern blot analysis revealed two major transcripts were expressed in brain and heart. Mouse BH-Pcdh-a mRNA was detected as a single band of approximately 5.5-kb. The mRNA level of mouse BH-Pcdh-a and -c were persistently detected by RT-PCR in developmental process of brain and heart, but that of mouse BH-Pcdh-b was elevated only in fetus and neonatal stage of brain. The chromosomal location of the mouse BH-Pcdh gene was determined as 5C3-D using fluorescence in situ hybridization.