Understanding how genetic variation is maintained within a species is important in ecology, evolution, conservation and population genetics. Tremendous efforts have been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played a major role since the 1990s. Here we describe a comprehensive database, varver (Variation in Vertebrates) that provides complete information regarding microsatellite variation in natural populations of vertebrates. For each species, varver includes basic information of the species, a list of publications reporting the microsatellite variation, and tables of genetic variation within and between populations (heterozygosity and FST). The geographic location and rough sampling range are also shown for each sampled population. The database should be useful for researchers interested in not only specific species but also comparing multiple species. We discuss the utility of microsatellite data, particularly for meta-analyses that involve multiple microsatellite loci from various species. We show that in such analyses, it is extremely important to correct for biases caused by differences in mutation rate, mainly due to repeat unit and number. It is an important task to understand how genetic variation is maintained within a species in ecology, evolution, conservation and population genetics. A tremendous amount of effort has been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played the major role since 1990'. We here develop a comprehensive database that provide full information of microsatellite variations in natural populations of vertebrates, named VarVer. For each species, VarVer includes basic information of the species, a list of publications that reported microsatellite variation, and tables of genetic variation within and between populations (heterozygosity and Fst). The geographic location and rough sampling range are also shown for each sampled population. The database should be useful for not only researchers who are interested in specific species but also those who are interested in comparing multiple species. We discuss how useful microsatellite data are particularly for meteanalyses that involve a number of microsatellite loci from various species. In such analyses, we show that it is extremely important to correct for biases caused by the difference in the mutation rate, mainly due to the repeat unit and number.