Objective To analyse the genetic polymorphisms of 19 autosomal STR loci in Han population of east, middle-northwest and southwest-south Shandong and to explore its genetic relationships among the population of these three regions. Methods STR loci of 1 044 unrelated Han individuals in three Shandong regions were typed with a Goldeneye?誖DNA ID System 20A kit. The allele frequency and population genetics parameters of 19 autosomal STR loci were statistically analysed by Modified-Powerstates software. The genetic distances among the population in three regions were calculated by Arlequin v3.5 software. The phylogenetic tree was conducted using MEGA v4.0 software. Results Fifteen of 19 autosomal STR loci were detected with the H values greater than 0.7, PIC values greater than 0.7, and DP values greater than 0.9 in the populations of all three Shandong regions. Among the populations in these three regions, the genetic distance between the populations in middle-northwest and southwest-south Shandong was closest （Fst=0.000 16）, followed by east and southwest-south Shandong （Fst=0.0003 6）. The genetic distance between the populations in east and middle-northwest Shandong was the farthest （Fst=0.000 66, P<0.05）. Conclusion The 19 autosomal STR loci show good genetic polymorphisms in Han population of three Shandong regions, and 15 of them are high. There are genetic differences between the populations in east and middle-northwest Shandong.