Models of host–parasite co-evolution suggest that parasites can exert frequency-dependent selection on their hosts, favouring rare alleles that confer resistance against widespread parasites and thus contributing to the maintenance of genetic variation, at some loci at least. If parasites are important in maintaining variation at many loci, then host species incurring a high prevalence of parasite infections should exhibit greater levels of genetic variation than host species incurring a lower prevalence. Using data from electrophoretic studies and from field surveys of haematozoan infections, we constructed a dataset including 103 species of North American and European birds to test this prediction. After controlling for sampling effort and phylogenetic influences, we found no relationship between parasite prevalence and either heterozygosity or polymorphism. These results do not support a role for parasites in the overall maintenance of genetic variation via frequency-dependent selection.