Dependence of plasma total homocysteine (tHcy) and DNA damage profiles on melanodialdehyde (MDA), oxidative stress, liver function tests (LFT), and lipids was studied in non-obese and obese subjects in the Pakistani population. Development of obesity is influenced by both genetic, biochemical and environmental factors. Plasma homocysteine (Hcy) and DNA damage profiles play a pivotal role in its progression. We studied 160 obesity patients and 160 lean subjects. Leukocytes were evaluated for DNA damage by comet assay and blood plasma for biochemical properties using commercial kits. Plasma Hcy level and DNA damage were strongly correlated with triglycerides (P < 0.000), LDL-cholesterol (P < 0.001), systolic blood pressure (P < 0.001), cholesterol (P < 0.004), MDA (P < 0.004) and total oxygen stress (P < 0.004) in obese individuals. Both Hyc and DNA damage were negatively associated with total anti-oxidant response and globulin. Both Hcy profile and DNA damage may have a role in the endothelium damage even in the normal range and are related to triglycerides, ALT, MDA, TOS, HDL- and LDL-cholesterol in the Pakistani population.