‘Microbranding’, a system for individually identifying reptiles and amphibians based on a numbered code of spot brands applied to the body and limbs, was tested on New Zealand skinks and geckos. Common geckos (Woodworthia maculata) and copper skinks (Oligosoma aeneum) were used as test animals. Brands applied in autumn took 3 months or more to heal. There was no evidence of brand-related mortality or increased parasite loads in branded animals. However, after healing the brands faded very rapidly in the skinks to become totally unreadable in all surviving branded skinks after 2.5 years and not accurately readable in most geckos after 3 years. We therefore consider the technique unsuitable as a standard marking procedure for New Zealand lizards.