In some organisms, their habitat can broadly predict their population genetic diversity. For example, marine fishes harbor considerably more genetic diversity than do freshwater fishes because of the larger long-term evolutionary effective population sizes in the former. Body mass (BM) is another predictor of genetic variation, in that small-bodied mammals generally have higher rates of molecular evolution than large mammals. Does genetic variation in birds vary similarly? We investigated the relationships among microsatellite DNA diversity, BM and habitat type (aquatic or terrestrial) in 76 avian species. Our results show that across 1008 avian microsatellite loci, mean heterozygosity was positively correlated with the number of alleles per species. The mean level of heterozygosity and allele number in birds were similar to those of mammals and reptiles, but smaller than fishes. Terrestrial birds have greater genetic diversity (both in terms of mean heterozygosity and allelic diversity per population) than aquatic species. BM of aquatic birds was significantly larger than that of terrestrial birds and there was a negative relationship between mean heterozygosity and BM. Our results, interpreted in light of previously published data from other vertebrates, suggest that patterns of genetic diversity in birds depends on their evolutionary effective population size (determined in part by ecological and environmental features) and on the rate of molecular evolution.