In this study, alterations in whole proteome expression patterns in the head of Japanese medaka (Oryzias latipes) was investigated following acute or chronic exposure to benzo(a)pyrene (BaP) (25 ${mu}g$ L$^{-1}$) for 48 hrs and 15 days, respectively. The results showed that 9 and 6 protein spots were statistically different, relative to controls, in response to acute and chronic BaP exposure, respectively. In the acute exposure group, 5 spots were up regulated and 4 spots were downregulated, while in the chronic exposure group, 4 spots were upregulated and 2 spots were downregulated. Three of these spots were common to both the acute and chronic BaP exposure groups and were identified using LC-MS/MS followed by database searching. These 3 spots were found to be associated with structural proteins belonging to the actin and keratin families. These data suggest that acute and chronic exposures to BaP may affect tissue morphology in the head of Japanese medaka.