Microsatellites are continuing to increase in popularity for genetic studies. A major drawback, however, is they often need to be isolated de novo. The traditional method (shotgun cloning) generally results in thousands of recombinant clones, which are then screened by Southern hybridization. Results are typically around 2% positive for mammals, but less than 0.4% for birds. Shotgun cloning is therefore generally not an effective method for isolating microsatellites from avian genomes. Several alternative methods have been developed, but the decision as to which method to use is often arbitrary. Here we present results for two microsatellite isolation techniques from four avian species.