Perfluorinated compounds (PFCs) have been used widely, detected worldwide in the environment, and have accumulated highly in animals. As far as we know, there have been no reports which relate the PFC concentration in wild animals to the physicochemical properties. Therefore, we measured the concentrations of 15 currently available PFCs (perfluorocarboxylic acids with x carbons: Cx, perfluorosulfonic acids with x carbons: CxS) in medaka and the environmental water where medaka live. Samples were obtained from 7 points in Japan (Iwate, Ibaraki, Niigata, Hyogo, Yamaguchi, Ehime, and Nagasaki) from July to September in 2013. Twenty to forty medaka were collected from each point, as well as 2 L of water in a clean PET bottle. PFCs were extracted and concentrated using a solid-phase cartridge, and were measured by LC/MS/MS. The medaka samples were treated individually. C5-C9 and C8S were detected mainly in the water, C11-C13 and C8S were detected mainly in medaka. C8S was always detected in high concentrations in the water and medaka. The bioconcentration factors (BCFs) of PFCs were calculated from PFC concentrations of the water and the medaka. The BCFs of C8-C11 were increased exponentially with the length of carbon chain. The BCF of C8S (approx. 5,500) was far greater than C8 (approx. 330) or C9 (approx. 480). However, the BCFs of C8-C11 and C8S tended to increase in proportion with octanol/water partition coefficient (log K_ow).