Microsatellites are ubiquitous throughout eukaryotic genomes and are useful in analyzing populations and genetic diversity. The QIAxcel system, an automated capillary electrophoresis device, allows the user to determine the size of microsatellite fragments, to discern allelic polymorphisms among individuals, and to differentiate homozygous and heterozygous individuals. This system provides comparable base pair resolution to more expensive systems at a relatively affordable cost.