Objective To screen the polymorphism in exon 3 and 9 of paired box4 (PAX4) gene and investigate the clinical characteristics of early-onset type 2 diabetes in Chinese. Methods Ninety-six patients with early-onset type 2 diabetes (early-onset diabetes group) and 100 people with normal results in oral glucose tolerance test (control group) were enrolled. PCR-direct sequencing was employed to detect polymorphism in exon 3 and 9 of PAX4 gene in two groups, and genotypic and allelic frequencies and clinical characteristics were statistically analysed.ResultsHis321Pro （A→C）polymorphism in exon 9 of PAX4 gene was detected in both groups, while no polymorphism was found in exon 3 of the gene. In comparison with control group, higher frequencies of CC genotype and C allele of His321Pro （A→C） polymorphism in exon 9 of PAX4 gene were detected in early-onset diabetes group, while there was no significant difference between groups (16.7% vs 11.0% and 41.1% vs 34.0%, P>0.05 for both). The frequencies of CC genotype and C allele of His321Pro （A→C） polymorphism in exon 9 of PAX4 gene in controls of this study were significantly lower than those in studies of Switzerland, Germany, Finland and Hungary (P<0.001). The fasting C peptide (FCP) levels of homozygous CC genotype carriers were significantly lower than those of AA and AC genotype carriers with His321Pro （A→C） polymorphism in exon 9 of PAX4 gene in early-onset diabetes group and control group （P<0.05）. Conclusion PAX4 gene polymorphism may not be the genetic susceptibility marker associated with the development of early-onset type 2 diabetes in Chinese. His321Pro （A→C）polymorphism in exon 9 of PAX4 gene may be associate with impaired fasting insulin secretion.