Inbreeding increases the level of homozygosity, which in turn might depress fitness. In addition, individuals having the same inbreeding coefficient (e.g. siblings) vary in homozygosity. The potential fitness effects of variation in homozygosity that is unrelated to the inbreeding coefficient have seldom been examined. Here, we present evidence from wild birds that genetic variation at five microsatellite loci predicts the recruitment success of siblings. Dyads of full–sibling great reed warblers (Acrocephalus arundinaceus), one individual of which became a recruit to the natal population while the other did not return, were selected for the analysis. Each dyad was matched for sex and size. Local recruitment is strongly tied to fitness in great reed warblers as the majority of offspring die before adulthood, philopatry predominates among surviving individuals and emigrants have lower lifetime fitness. Paired tests showed that recruited individuals had higher individual heterozygosity and higher genetic diversity, which was measured as the mean squared distance between microsatellite alleles (mean d2), than their non–recruited siblings. These relationships suggest that the microsatellite markers, which are generally assumed to be neutral, cosegregated with genes exhibiting genetic variation for fitness.