The protocadherins are a subfamily of the calcium-dependent cell-cell adhesion and recognition proteins of the cadherin superfamily. In this study we describe the isolation and characterization of two novel protocadherins, PCDH8 and PCDH9, that constitute a new linkage group on human chromosome 13 and mouse chromosome 14. Like other protocadherins both genes are predominantly expressed in brain, but PCDH9 is also expressed in a broader variety of tissues, and the expression patterns appear to be developmentally regulated. We have determined the genomic organization of PCDH8, which differs significantly from that of the other cadherin subfamilies. In contrast to the classical and desmosomal cadherins, which in general consist of 15-17 exons and share a remarkable degree of conservation in intron position, PCDH8 consists of only three exons and lacks introns in the extracellular domain. The first exon encodes the extracellular domain, the transmembrane region, and part of the cytoplasmic tail. The second exon encodes the remainder of the cytoplasmic region and is partially untranslated. The differences in the genomic structure of cadherin subfamilies will be discussed in the context of the evolution of the cadherin superfamily.