Abstract. The aim of the present study was to investigate the association of human leukocyte antigen (HLA) gene polymorphism and clinical phenotypes of patients with mesangial proliferative glomerulonephritis (MsPGN). The genotyping of HLA-A, HLA-B and HLA-DRB1 alleles was detected in 1,536 consecutive MsPGN patients during the previous five years and 2,027 age-and gender-matched healthy individuals by using the polymerase chain reaction-sequence-specific primers method. The clinical and pathological data of the patients were collected and the genotype frequencies (GF) and odds ratio (OR) were analyzed. The allele frequencies of HLA-A*23, A*25, B*15, B*40, B*53 and DRB1*18 were significantly higher in MsPGN patients than in the controls (P<0.05). These alleles were considered as the suspected susceptibility genes (SSG) for MsPGN. Of note, results of the follow-up survey study demonstrated poorer prognosis of patients with SSG than those without SSG.