Nucleotide repeats (microsatellites) mapped to specific locations on each chromosome are used to evaluate genomic polymorphism. From 23 microsatellites we selected eleven that were variant in PCR amplimer size between CD-1 colony and NOD or NOR strains. We used these microsatellites to identify individuals that were used for backcrossing, thus accelerating the acquisition of a new genetic background. Results yield a defined analysis of the genome in question and profiles were compared to detect genetic variation among individuals. After the selection of mice for backcrossing at the third generation, the 11 specific markers were acquired at the 5th generation and maintained to the 10th generation. Diabetes incidence and insulitis score correlated with the acquisition of genetic background, demonstrating that using this strategy, 5? crosses are enough to obtain the genotype of interest, shortening the process in more than one year and a half.