Indoleamine 2,3-dioxygenase 1 (IDO1) catabolizes tryptophan to kynurenine at the first step of tryptophan metabolism. Recently, in addition to IDO1, a new isoform called IDO2 was identified. In this study, we examined the tissue expression pattern of IDO2 mRNA and the cellular localization of expressed IDO2 protein in mice. IDO1 mRNA expression was observed in the colon and epididymis, whereas IDO2 mRNA expression was found in the cerebral cortex, liver, kidney, and epididymis. Immunohistochemical analysis revealed that IDO2 protein was exclusively expressed on the hepatocytes, interlobular bile ducts, neuronal cells of the cerebrum cortex, Purkinje cells of the cerebellum cortex, lamina epithelialis, proximal convoluted tubule, and the collecting tubule of the kidney. In the epididymis, IDO1 protein expression was restricted to the caput, whereas IDO2 protein expression was observed on the caput, corpus, and cauda. Both IDO proteins were expressed on the caput, but both showed a different protein expression pattern in the segments. Immunohistochemical analysis in IDO1(-/-) mouse epididymis showed that IDO2 protein was extensively upregulated due to the loss of IDO1 expression.