WNT signals, transduced through Frizzled (FZD) receptors with extracellular WNT-binding domain and cytoplasmic Dishevelled-binding domain, are implicated in carcinogenesis and embryogenesis. WNT3-WNT9B (WNT14B) locus (17q21.31) and WNT3A-WNT9A (WNT14) locus (1q42.13) are paralogous regions within the human genome. Here, the rat Wnt3 and Wnt9b genes were identified and characterized by using bioinformatics. Wnt3 and Wnt9b genes at rat chromosome 10q32.1 were clustered in head-to-head manner with an interval of about 24 kb within AC105632.3 genome sequence. The rat Wnt3 gene, consisting of five exons, encoded a 355-aa protein with N-terminal signal peptide, 24 conserved Cys residues and two Asn-linked glycosylation sites. The rat Wnt9b gene, consisting of four exons, encoded a 359-aa protein with N-terminal signal peptide, 24 conserved Cys residues and one Asn-linked glycosylation site. The rat Wnt3 core promoter showed 80.5% nucleotide identity with human WNT3 core promoter, while rat Wnt9b core promoter showed 45.6% nucleotide identity with human WNT9B core promoter. MYB (c-Myb), ELK1, POU2F1 (OCT1), HNF4A (HNF-4), COMP1, NFYA (NF-Y) and NKX2-5 binding sites were conserved between rat Wnt3 and human WNT3 core promoters. The Wnt3-Wnt9b intergenic conserved region (IGCR), corresponding to nucleotide position 124747-125252 of AC105632.3 genome sequence, showed 85.6% nucleotide identity with human WNT3-WNT9B IGCR. GC content of rat Wnt3-Wnt9b IGCR was 59.5%. Wnt3-Wnt9b IGCR was predicted as regulatory element rather than gene because cDNA or EST derived from Wnt3-Wnt9b IGCR was not identified. This is the first report on the rat Wnt3 and Wnt9b genes as well as on comparative genomics on the Wnt3-Wnt9b gene cluster.