Body condition is important because it is correlated with population and habitat quality parameters. Since the direct measurements are either lethal or unreliable, a wide range of non-lethal body condition indices has been proposed. The aim of our study was to apply and compare three body condition indices (Fulton's index, relative body condition mass index and residual index) using body size indicator – body mass data for 24 populations of the yellow bellied toad (Bombina variegata). The condition index should be independent of body size indicator, in this case snout vent length (SVL). Therefore we tested all three indices for the statistical independence of SVL and for the normality of distribution. Fulton's index violated the independence assumption, whereas the relative body condition mass index did not have a normal distribution. Residual index was found both independent of SVL and normally distributed. Moreover, the residual index highlighted biological significant differences on the basis of altitude and season. Our results recommend the residual index as a useful tool in amphibian monitoring and conservation.