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Introduction: The study was carried out to identify the polymorphisms in mitochondrial genes (ATPase and ND1) in type 2 Diabetes Mellitus (T2DM) from Mizo population and to correlate the involvement of demographic factors. Findings: In the present study, 58 patients and 50 healthy volunteers were considered. The mutations observed were mostly base substitutions and were similar as reported for other populations. Three mutations are unreported and were found to be novel polymorphisms for diabetic disease. One heteroplasmic variation (MT3970 C > T) was found in 36.36% of samples. Subjects with excessive smoked meat consumption and customary habit of smoking (ORs: 4.92; 95% CI: 0.96-25.21) were found to be more prone to T2DM. Mitochondrial genes sequence analysis revealed the genetic variability between the healthy and diabetic samples. Conclusion: Mitochondrial ATPase and ND1 gene polymorphisms may be involved in triggering the risk for T2DM. [ABSTRACT FROM AUTHOR]