Medaka (Oryzias latipes) is a teleost fish with an XX/XY sex determination system, similar to that of mammals. However, under high temperature conditions, XX medaka is masculinized by elevation of cortisol, the major teleost glucocorticoid. Previously, the RNA-seq analysis showed that expression of peroxisome proliferator-activated receptor alpha (PPARa) signalling genes was increased by cortisol. In this study, to identify PPARa target genes during sexual differentiation, we performed ChIP-seq analysis using medaka larvae.