The protein-coding region of the mouse patched gene Ptch2 was cloned and its expression was studied. The open reading frame was predicted to encode 1182 amino acids. The protein contained 12 transmembrane domains and 2 large extracellular loops. In comparison with other members of the patched protein family, Ptch2 showed divergence in the hydrophilic region and in the amino- and carboxy-terminal regions. Ptch2 lacked a conserved C-terminal element which is found in mouse Ptch, human PTCH and chick Ptc but not in zebrafish Ptc1 and Drosophila Ptc. Mouse Ptch2 shared 64% amino-acid identity with zebrafish Ptc1 but only 56% with mouse Ptch. It is suggested that mouse Ptch2 is an orthologue of zebrafish Ptc1. Ptch2 has been mapped to chromosome 4 and is unlinked to Ptch on chromosome 13. Ptch2 was weakly expressed in early embryos in a pattern overlapping that of Ptch. Ptch was expressed strongly in mesenchymal condensations surrounding the epidermal invaginations of developing tooth buds, hair follicles and whiskers adjacent to epithelial cells expressing sonic hedgehog (Shh). Ptch2 transcripts were detected only in the invaginating epithelial cells. In mice lacking a functional GLi2 zinc-finger protein gene, a part of the Shh regulatory cascade, Ptch and Ptch2 were both down-regulated, which indicated that expression of both Ptch genes was modulated by Shh. The nucleotide sequence of Ptch2 has been submitted to the EMBL and NCBI databases with accession number AB000847.