Abstract Extensive cDNA analysis demonstrated that all human and mouse protocadherin-β genes are one-exon genes. The protein sequences of these genes are highly conserved, especially the three most membrane-proximal extracellular domains. Phylogenetic analysis suggested that this unique gene family evolved by duplication of one single protocadherin-β gene to 15 copies. The final difference in the number of protocadherin-β genes in man (#19) and mouse (#22) is probably caused by duplications later in evolution. The complex relationship between human and mouse genes and the lack of pseudogenes in the mouse protocadherin-β gene cluster suggest a species-specific evolutionary pressure for maintenance of numerous protocadherin-β genes.