Published studies of wild vertebrate populations have almost universally reported positive associations between genetic variation measured at microsatellite loci and fitness, creating the impression of ubiquity both in terms of the species and the traits involved. However, there is concern that this picture may be misleading because negative results frequently go unpublished. Here, we analyse the relationship between genotypic variation at nine highly variable microsatellite loci and neonatal fitness in 1070 Antarctic fur seal pups born at Bird Island, South Georgia. Despite our relatively large sample size, we find no significant association between three different measures of heterozygosity and two fitness traits, birth weight and survival. Furthermore, increasing genetic resolution by calculating parental relatedness also yields no association between genetic variation and fitness. Our findings are consistent with necropsy data showing that most pups die from starvation or trauma, conditions that are unlikely to be influenced strongly by genetic factors, particularly if the benefits of high heterozygosity are linked to immune-related genes.