Objective To analyse the genetic polymorphism of 21 autosome STR loci in Han population of Shandong Province and the cases with loci mutation or allelic loss typed by Goldeneye?誖DNA identification system 25A. Methods Totally 40 autosome STR loci types of 273 unrelated individuals in Han population of Shandong Province were typed by Goldeneye?誖DNA identification system 25A and 22NC, and the genetic polymorphism of 21 STR loci in those was analysed. Meanwhile, six cases with loci mutation were analysed by adding the tests with Goldeneye?誖DNA identification system 22NC, 20Y and 17X. Another three cases with allelic loss were tested by AmpF?詛STR?誖Identifiler?誖Plus PCR and analysed by gene sequencing. Results The genetic parameters of 21 autosome STR loci in Han population of Shandong Province were obtained. When STR loci were added up to 40, five of those with loci mutation met the identification requirements, and the results of X-STR or Y-STR types were consistent with that of STR loci. There was another duo case with one suspected loci mutation, biological source of six STR loci genotypes could not be found in the genotypes of supposed father. The Y-STR genotype of two individuals was identical that indicated both of them came from same paternal line. However, the fatherhood was excluded according to the autosome STR loci system. For two cases with allelic loss on D18S51, base mutation or loss were found in the primer binding domain of mother and child by gene sequencing. Another mother-child case with allelic loss on D13S317 was certified by AmpF?詛STR?誖Identifiler?誖Plus PCR kit. Conclusion The 21 autosome STR loci in Han population of Shandong Province have high polymorphism, which can be used in routine cases of paternity identification. For some duo cases with loci mutation, Goldeneye?誖DNA identification system 25A cannot satisfy the identification requirements, thus more autosome STR loci should be added properly. For the cases with allelic loss, the problem can be resolved by gene sequencing or using different merchant kits.