In a teleost fish, the medaka (Oryzias latipes), many inbred strains have been established from various origins including wild populations. Brains from five genetically different strains, which had been bred and raised under the same conditions, were examined to determine whether there is intraspecific genetic variation. A total of 25 brains from the wild-type strains (HNI-II, HB11A and HB32C) and from the body-colour mutant strains (Hi3 and HO5) were fixed, and the external features of the brains were examined under a stereomicroscope. The differences between the HNI-II brains and the Hi3 brains were the most remarkable in the external features. In order to carry out a volumetric analysis, the brains of all strains were cut into complete serial cryostat sections. Total brain volumes and relative volumes (in % of total brain volume) of the olfactory bulb, telencephalon, optic tectum, and cerebellum were calculated in each brain using a semi-automatic image analyzer. Statistical analysis showed that significant differences in the total brain volumes and the relative volumes of these subdivisions exist not only between wild-type and mutant strains but also among wild-type strains. Thus, our results demonstrate that the strains with different genotypes possess large variation in brain morphology. This is the first report to demonstrate that there exists intraspecific genetic variation in the gross brain morphology of a wild-type vertebrate.