Objective To test and analyze the genetic background of highly immunodeficient mice from different sources. Methods Four highly immunodeficient mouse strains from different sources of NOD background were collected. 30 microsatellite DNA sites were detected, and the genotype can be displayed by gel electrophoresis and STR scanning. Results 17 microsatellite sites exhibit polymorphism in 20 mice of the four groups. There were 30 homozygous loci in the mice of groups A and B, and heterozygous in the other two groups. The genetic distance is minimum between groups A and B, showing a higher genetic similarity. Conclusions The genetic backgrounds are different in highly immunodeficient mice from different sources.