Abstract: Objective　To investigate association of the paired box 4 (PAX4) gene rs3824004 (574C>A; R192S) and rs2233580 (575G>A; R192H) polymorphism with obesity and metabolic markers in children and adolescents. Methods　A total of 103 obese children were randomly selected, and an average age was (10.82±2.57) years, and body mass index (BMI) was (26.82±4.57) kg/m2. At the same period, 100 normal weight children were selected as the control group, and an average age of (10.60±2.84) years, and BMI was (16.79±2.13) kg/m2. The blood pressure, physical measurements, and blood metabolic parameters were measured and compared. The oral glucose tolerance test (OGTT) and insulin release test were performed in the obesity group. The homeostasis model insulin resistance index (HOMA-IR) and the overall insulin sensitivity index (WBISI) were calculated. PAX4 rs3824004 and rs2233580 polymorphism were detected by PCR. The differences of allele frequency and genotype frequency of polymorphic loci were analyzed, and the correlation between different genotypes and metabolic indexes was analyzed. Results　The height, weight, BMI, systolic blood pressure, diastolic blood pressure, waist circumference, hip circumference, waist to height ratio (WHtR), fasting blood glucose (FPG), total cholesterol (TC), low density lipoprotein (LDL), triacylglycerol (TG), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) in the obesity group were significantly higher than those in the control group, and the high density lipoprotein (HDL) was significantly lower than that in the control group (all P<0.05). The frequency of gene distribution was in accordance with the Hard-Weinberg balance. The frequencies of A allele of rs3824004 in obesity and control groups were 4.9% and 5.0%, respectively, and the frequencies of CA genotype were 9.7% and 10.0%, respectively, and there was no significant difference between two groups (P>0.05). The frequency of GA allele of rs2233580 in obesity group was 25.2%, which was significantly higher than that in control group (P<0.05). The BMI and waist in rs2233580 GA genotype were significantly higher than those in GG genotype (all P <0.05). However, logistic regression analysis showed that there was no correlation between PAX4 rs2233580 genotype and metabolic markers (all P>0.05). There were no significantly differences in HOMA-IR and WBISI among different genotypes of PAX4 rs2233580 in obesity group (all P>0.05). Conclusions　PAX4 rs2233580 affects children's BMI and waist circumference and may be involved in the development of childhood obesity, but it is not an independent risk factor for obesity in children and adolescents.