Members of the Toll-like receptor family 9 (TLR9) subfamily sense viral and bacterial DNA present in the endosomal compartment. Here we describe the cloning and regulation of a TLR9 gene from Atlantic salmon (Salmo salar). The salmon TLR9 cDNA encodes 1075 amino acids and analysis of the inferred protein sequence shows that several amino acid residues known to be important for the functions of TLR9 in mammals are conserved in salmon. Furthermore, TLR9 expression was elevated in head kidney leukocytes after in vitro treatment with CpG ODNs and recombinant trout interferon (IFN)-γ. IFN-γ was the strongest inducer of TLR9 expression. Together, the results indicate that the structure, the expression and possibly the function of TLR9 are conserved across the teleost and mammalian lineages.