Recent evidence suggests that marker-based heterozygosity-fitness correlations may be driven by only one or a few markers, indicating local heterozygosity effects caused by linkage disequilibrium with functional genes. In this study, we investigated the relationship between microsatellite heterozygosity and a measure of cell-mediated immunity (phytohaemagglutinin; PHA) in bluethroat (Luscinia s. svecica) nestlings using a full-sibling design. We found significant positive associations between PHA response and two different indices of microsatellite heterozygosity, i.e. multi-locus heterozygosity and mean d(2). However, model comparisons disclosed that both associations were more likely caused by local effects rather than general effects and that the two local effects appeared to be realized through two different genetic mechanisms. Our results indicate that both the random assortment of parental chromosomes during meiosis as well as inbreeding can drive heterozygosity-fitness correlations.