WNT and Hedgehog signaling pathways are implicated in various types of human cancer, such as gastric and pancreatic cancer. WNT1, WNT2, WNT2B (WNT13), WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A (WNT14), WNT9B (WNT14B). WNT10A, WNT10B, WNT11 and WNT16 genes encode WNT family glycoproteins, which transduce signals through Frizzled (FZD) family receptors with extracellular WNT-binding and cytoplasmic Dishevelled-binding domains. WNT6 and WNT10A genes at human chromosome 2q35 are clustered in tail-to-head manner with an interval of <7 kb. Here, we identified and characterized rat Wnt6 and Wnt10a genes by using bioinformatics. Wnt6 and Wnt10a genes were clustered in tail-to-head manner with an interval of about 7 kb within AC127107.3 and AC132020.3 genome sequences. Rat Wnt6 gene, consisting of four exons, encoded a 365-aa protein with signal peptide, 24 conserved Cys residues, two Asn-linked glycosylation sites and an RGD motif. Rat Wnt10a gene, consisting of four exons, encoded a 417-aa protein with 24 conserved Cys residues, two Asn-linked glycosylation sites and an RGD motif. Rat Wnt6 and human WNT6 showed 97.8% total-amino-acid identity, while rat Wnt10a and human WNT10A showed 95.4% total-amino-acid identity. Promoter region was conserved between rat Wnt6 and human WNT6 genes. GATA, FOXA2, and TGIF binding sites were located within the conserved region of rat Wnt6 and human WNT6 promoters. This is the first report on rat Wnt6 and Wnt10a genes as well as on the conserved promoter region of Wnt6 orthologs.