Single-nucleotide polymorphisms (SNPs) in MYH9-APOL1 gene regions have been reported to be associated with diabetic kidney disease (DKD) in the American population. We examined the association between polymorphisms in MYH9-APOL1 and DKD susceptibility in a Chinese Han population. MYH9 rs3752462 (T>C) and APOL1 rs136161 (C>G) were genotyped in 303 DKD patients and 364 type 2 diabetes mellitus (T2DM) patients without kidney disease using the TaqMan SNP genotyping assay. Chi-squared test and multivariate logistic regression were used to evaluate the association. We observed that only MYH9 rs3752462 was associated with DKD (genotype, P = 0.004; allele, P = 0.002). Genetic model analysis revealed that rs3752462 was associated with increased risk of DKD under a dominant model adjusted by age and sex (adjusted odds ratio (aOR), 1.675; 95% CI 1.225-2.289; P = 0.001) and an additive model (TC versus TT: aOR, 1.649; 95% CI 1.187-2.290; CC versus TT: aOR, 1.817; 95% CI 0.980-3.367; P = 0.005). The combined effect of rs3752462 TC + rs136161 CC genotype showed an association of DKD adjusted by age and sex (aOR, 1.732; 95% CI 1.128-2.660; P = 0.012). After a Holm-Bonferroni correction for multiple tests, the C allele frequencies of the rs3752462 and the TC + CC genotype in the dominant model were considered statistically significant with a markedly increased risk of DKD (P < 0.00208; P < 0.002). Our results suggest that MYH9 rs3752462 is significantly associated with an increased risk of DKD in Chinese Han individuals.