Populations of sand lizards (Lacerta agilis) are declining throughout its north-western range. Here we characterize fifteen new microsatellite markers developed specifically for parentage analysis in a small Swedish population of sand lizards. These loci were screened in the Asketunnan population and a much larger and genetically diverse Hungarian population, with heterozygosities ranging from (0.217–0.875) and (0.400–0.974), respectively. All loci were in Hardy-Weinberg Equilibrium in the Swedish population but eight loci had significant heterozygote deficiencies in the Hungarian population. Two loci were significantly linked in both populations. These microsatellite loci are likely to be applicable in research on other sand lizard populations throughout Europe.