Toll-like receptor 3 (TLR3), an antiviral innate immunity receptor recognizes double-stranded RNA, preferably of viral origin and induces type I interferon production, which causes maturation of phagocytes and subsequent release of chemical mediators from phagocytes against some viral infections. The present study has characterized TLR3 complementary DNA (cDNA) in buffalo (Bubalus bubalis) and nilgai (Boselaphus tragocamelus). TLR3 coding sequences of both buffalo and nilgai were amplified from cultured dendritic cell cDNA and cloned in pGEMT-easy vector for characterization by restriction endonucleases and nucleotide sequencing. Sequence analysis reveals that 2,715-bp-long TLR3 open reading frame encoding 904 amino acids in buffalo as well as nilgai is similar to that of cattle. Buffalo TLR3 has 98.6 and 97.9% identity at nucleotide level with nilgai and cattle, respectively. Likewise, buffalo TLR3 amino acids share 96.7% identity with cattle and 97.8% with nilgai. Non-synonymous substitutions exceeding synonymous substitutions indicate evolution of this receptor through positive selection among these three ruminant species. Buffalo and nilgai appear to have diverged from a common ancestor in phylogenetic analysis. Predicted protein structures of buffalo and nilgai TLR3 from deduced amino acid sequences indicate that the buffalo and nilgai TLR3 ectodomain may be more efficient in ligand binding than that of cattle. Furthermore, TLR3 messenger RNA expression in tissues as quantified by real-time PCR was found higher in nilgai than buffalo.