Vipera ursinii rakosiensis is the most endangered venomous snake in Europe. Our information on the state of natural populations is somewhat limited apart from recent results indicating high genetic diversity in all of its three major areas in the Carpathian Basin. Developmental instability (DI) is a good indicator of environmental or internal perturbations an individual experiences during development, and fluctuating asymmetry (FA; random deviations from bilateral symmetry) is a good proxy for DI. We studied FA in head scale numbers in V. u. rakosiensis populations and contrasted it with the FA of other subspecies. The four V. u. rakosiensis populations showed similar FA levels. The FA in V. u. rakosiensis was higher than in the V. u. moldavica and V. u. ursinii populations, but similar to the V. u. macrops population. The (not exceptionally) high FA in V. u. rakosiensis might indicate external or internal stressors increasing DI. We suggest that FA should be monitored to get information on changes in DI.