Protocadherins are predominantly expressed in the nervous system, and constitute the largest subgroup within the cadherin superfamily. The recent structural elucidation of the amino-terminal cadherin domain in an archetypal protocadherin revealed unique and remarkable features: the lack of an interface for homophilic adhesiveness found in classical cadherins, and the presence of loop structures specific to the protocadherin family. The unique features of protocadherins extend to their genomic organization. Recent findings have revealed unexpected allelic and combinatorial gene regulation for clustered protocadherins, a major subgroup in the protocadherin family. The unique structural repertoire and unusual gene regulation of the protocadherin family may provide the molecular basis for the extraordinary diversity of the nervous system.