Diabetic autonomic neuropathy (DAN) is a serious and common complication of diabetes, often overlooked and misdiagnosed. It is a systemic–wide disorder that may be asymptomatic in the early stages. The pathogenesis is still unclear and probably multifactorial. The most and clinically important form of DAN in diabetes is genetic studies. Hence the aim of the present study is to evaluate biochemical and molecular studies on subjects with diabetes and autonomic neuropathy. Fifty five diabetic subjects as study subjects and twenty two healthy subjects without any chronic illness as control were selected for the present study. The extent of somatic DNA damage is quantified by Cytokinesis Block Micronuclei (CBMN) assay. Detailed demographic and clinical characteristics were recorded and compared. The present study demonstrated that micronuclei frequency was significantly elevated in the study subjects than control subjects. A positive correlation between micronuclei frequency and various risk factors showed increased genetic instabilities. Prevention strategies are based on strict glycemic control with intensive insulin treatment, multifactorial intervention and lifestyle modification.