Ethics committees that are required to oversee research activities involving the capture and handling of wild animals tend to take a cautious attitude because little has been published that quantifies their effects on animals. However, to address questions in ecology and evolution, it is often essential to be able to identify individual animals. Toeclipping is one of the most commonly used marking techniques for individual identification of amphibians and reptiles. The effects of toe-clipping on survival have not been well studied. We used Cormack-Jolly-Seber mark-recapture models to estimate apparent survival (Φ) and the recapture probability (p) of an arboreal gecko species (Gehyra variegata) and a ground dwelling skink (Morethia boulengeri). We captured 551 geckos and 359 skinks over 12 y, individually marked them by clipping 1–7 toes, and we classified them as juvenile, sub-adult, or adult (stage). In G. variegata, the most parsimonious model included stage as the only factor affecting survival and year affecting capture probability. The best supported model that included the number of toes as a covariate was less than half as likely (ΔQAICc = 2.02) but still had a weight of 0.2. Hence, there is a probability that the number of toes clipped had an effect on survival, with the number of toes negatively affecting survival in juveniles and subadults. In M. boulengeri, the most parsimonious model was constant apparent survival rates and capture probabilities. There was no evidence of an effect of the number of toes clipped on survival probability.