The relationship between individual genetic diversity and fitness-related traits are poorly understood in the wild. The availability of highly polymorphic molecular markers, such as microsatellites, has made research on this subject more feasible. We used three microsatellite-based measures of genetic diversity, individual heterozygosity H, mean d(2) and mean d(2) (outbreeding) to test for a relationship between individual genetic diversity and important fitness trait, juvenile survival, in a population of alpine marmots (Marmota marmota), after controlling for the effects of ecological, social and physiological parameters that potentially influence juvenile survival in marmots. Analyses were conducted on 158 juveniles, and revealed a positive association between juvenile survival and genetic diversity measured by mean H. No association was found with mean d(2) and with mean d(2) (outbreeding). This suggests a fitness disadvantage to less heterozygous juveniles. The genetic diversity-fitness correlation (GDFC) was somewhat stronger during years with poor environmental conditions (i.e. wet summers). The stressful environmental conditions of this high mountain population might enhance inbreeding depression and make this association between genetic diversity and fitness detectable. Moreover the mating system, allowing extra pair copulation by occasional immigrants, as well as close inbreeding, favours a wide range of individual genetic diversity (mean H ranges from 0.125 to 1), which also may have facilitated the detection of the GDFC. The results further suggest that the observed GDFC is likely to be explained by the "local effect" hypothesis rather than by the "general effect" hypothesis.