Methods to measure and monitor wild populations are important conservation tools in areas affected by anthropogenic disturbances. We compared three populations of the South American frog Physalaemus cuvieri Fitzinger, 1826 (Leptodactylidae) from areas with different degrees of anthropogenic disturbance in regard to their degrees of fluctuating asymmetry (FA). We selected four morphological characters (radio-ulna, femur, tibia-fibula and digit length) and compared two populations from relatively pristine areas with one population located in a highly urbanised and disturbed area. We found a significantly higher level of FA for the digit length, p < 0.05, in the population suffering the highest level of anthropogenic disturbance in relation to the two populations located in the pristine areas. There are no significant differences in the three populations in regard to FA for the radio-ulna, femur and tibia-fibula. The absence of FA in these three measurements might indicate a negative effect of limb asymmetry on this species survivorship. Our study provides a good example of the use of FA as indicator of environmental stress. However, this result must be viewed with some caution, since we observed FA in only one morphological character.