Interleukin-1 receptor-associated kinase 4 (IRAK-4) is an important component of the mammalian innate and adaptive defense system against infectious disease. In this study, ayu Plecoglossus altivelis altivelis IRAK-4 cDNA and genomic DNA were cloned and analyzed. The open reading frame of ayu IRAK-4 cDNA encodes 463 amino acids, including a death domain and a serine/threonine protein kinase domain of the mammalian IRAK-4 motif. The ayu IRAK-4 gene comprises 11 exons, and was found to be very similar to vertebrate IRAK-4 genes described thus far. Ayu IRAK-4 mRNA was expressed in all tissues, and predominantly in the gill, heart, intestine, whole kidney, and spleen. At 12 h after immersion challenge with Flavobacterium psychrophilum, ayu IRAK-4 mRNA expression in the whole blood was up-regulated (21.6-fold) compared to the control. The present study suggests that ayu IRAK-4 may be involved in the immune response.