Although females' mating with multiple males is widespread in socially monogamous species, its evolutionary significance is poorly understood. Tests of the hypothesis that socially monogamous females seek extra-pair copulations to increase the heterozygosity of their offspring have produced mixed results. Some of the inconsistency may be the result of technical limitations of the molecular analyses used. In a previous analysis using five microsatellite loci, we showed that in the House Wren (Troglodytes aedon) extra-pair sires had fewer alleles common to the population than did other nearby males that could have sired offspring but did not, suggesting a “rare male” effect (Masters et al. 2003, Proceedings of the Royal Society of London, Series B 270:1393–1397). We repeated the previous analysis, including an additional set of seven microsatellite loci. An analysis that used all 12 loci (both the original and additional loci) produced results suggesting that genotype affects extra-pair paternity. By contrast, an analysis using only the seven new loci alone showed no significant effects. We conclude that studies of this type are likely to be sensitive to the loci employed, particularly when relatively low numbers of loci are analyzed.