this study investigated the correlation of four single nucleotide polymorphisms (Snps) in Apolipoprotein M (ApoM) with the risk of type 2 diabetes mellitus (T2DM) and effects of the interactions of this gene and obesity. The effects of SNP and obesity interaction on T2DM was examined by generalized multifactor dimensionality reduction (GMDR) combined with the logistic regression model. T2DM patient-control haplotype was analyzed in silico using the haplotype analysis algorithm SHesis. The rs805296-C allele or 724-del allele indicted high risk of T2DM. The incidence of T2DM in individuals with rs805296-C allele polymorphism (TC + cc) was higher than those without (tt), adjusted oR (95%CI) = 1.29 (1.10-1.66) (p < 0.001). Moreover, the individuals with 724-delallele have a higher risk of T2DM compared to those with 724-ins variants, adjusted OR (95%CI) = 1.66 (1.40-2.06), p < 0.001. GMDR analysis suggested that the interaction model composed of the two factors, rs805296 and obesity, was the best model with statistical significance (P value from sign test [P sign ]=0.0107). The T2DM risk in obese individuals having TC or CC genotype was higher than non-obese individuals with tt genotype (oR = 2.38, 95% CI = 1.58-3.53). Haplotype analysis suggests that rs805297-C and rs9404941-C alleles haplotype indicate high risk of T2DM, OR (95%CI) = 1.62 (1.29-2.16), p < 0.001. Our results suggested that rs805296 and 724-del minor allele of ApoM gene, interaction of rs805296 and obesity, rs805297-C and rs9404941-C alleles haplotype were indicators of high T2DM risk. Among adults in China, the estimated overall prevalence ofdiabetes was 10.9%, and that for prediabetes was 35.7%. Thus, the prevalence of type 2 diabetes mellitus (T2DM) in China is the highest in the world 1 , and the number of patients with T2DM will be about 438 million in 2030 2,3. Unfortunately, the incidence of T2DM will continue to increase in the next decades in many countries, including China, due to longevity of human life and obesity 4. The development and progression of T2DM are believed to be closely correlated with the interaction of multiple susceptibility genes and gene interactions with the environment 5-7. Human apolipoprotein M gene is structurally conserved across species and located at the human chromosome 6p21.33 8,9. ApoM is reported to be highly expressed in liver and kidneys, but weakly expressed in other human tissues 10. Previous studies reported associations between ApoM gene variations and human diseases, including CAD and T2DM; however, these observations remain controversial 11-15. In Chinese populations, Xu et al. 11 showed the ApoM rs9404941 (T-855C) polymorphism predicts a high incidence of CAD. Furthermore, ApoM rs805296 (T-778C) polymorphism was closely related with the incidence of either type 1 or type 2 diabetes 12,13. However, the association of Apo Mgene polymorphism in rs805296 (T-778C) and the risk of T2DM was found in another independent study based on Southern Chinese population 14. Emerging evidence showed that genetic and ...