In the Monte region of Argentina, the local population is causing severe habitat degradation by extracting native vegetation and domestic animal grazing. To assess whether disturbed environments have higher levels of asymmetry than control environments, we examined morphological variation and fluctuating asymmetry in the cephalic region of the longtail whiptail lizard Aurivela longicauda (Teiidae) using a Procrustes analysis with geometric morphometry. This is the first study of asymmetry using geometric morphometry in a lizard from Argentina. While there was no difference in the size of the cephalic region between the two environments, there were differences in shape between the right and left side of the lizard's head (object symmetry), the differences being greater at disturbed sites (fluctuating asymmetry), suggesting that anthropogenic activities may act as stressors driving alterations in the fitness (reproduction) of reptile populations. Fluctuating asymmetry analysis is an excellent conservation biology and environmental monitoring tool for measuring stress in different organisms.