Using polymerase chain reaction and denaturating polyacrylamide gel electrophoretic techniques, we studied 53 cases of hydatidiform moles. Of these, 41 cases were genetically complete hydatidiform moles (g-CHM) whose genome were totally paternally derived. We investigated the distribution of the alleles in the short tandem repeat sequences at loci D16S539, D7S820, and D13S317 in these cases. In particular, we analyzed the allelic distribution and potential significance in cases with traceable benign and invasive moles (i.e., persistent trophoblastic tumor [PTT]). Among 41 g-CHM cases, there were six alleles at D16S539, five alleles at D7S820 (the frequencies of alleles 9 and 10 were respectively lower and higher than those in Beijing population), and seven alleles at D13S317; the heterozygosity of loci D16S539, D7S820, and D13S317 was 0.0732, 0.0976, and 0.0732, respectively. Among 23 benign cases, there were six alleles at D16S539, four at D7S820, and six at D13S317; among 11 PTT cases, there were five alleles at D7S820 and four alleles each at D16S539 and D13S317. The frequencies of allele 9 at D16S539 and allele 10 at D7S820 were higher than in benign cases (P < 0.05). There were significant differences in frequencies of alleles 9 and 10 at D7S820 between the cases and the Beijing population, and heterozygosity at the three loci was lower in the cases than in the population. In addition, invasiveness of hydatidiform mole correlated to the frequency of allele 9 at loci D16S539 and allele 10 at D7S820.