SSR fingerprints were analyzed in three generations of fat line (FL) and lean line (LL) of broiler chickens. Changes in gene frequencies of every locus were evaluated. Thus the relationship between SSR markers and VLDL (a trait representing fat mass of broiler), which is the basis for early selection of LL broiler, was examined. Fourteen microsatellite locus were successfully amplified with 4 of 5 primers used. The results of chi2 test for the gene frequencies of every locus show that one locus was significantly different in generation 1(P<0.05), two in generation 2 and 4 in generation 3.