The aim of this study was to determine the association of Gly482Ser variant of proliferator activator receptor γ coactivator 1α (PPARGC1α) gene with diabetes in Pakistani population. A total of 900 blood samples (diabetic=451, controls=449) were genotyped by PCR-RFLP. A significant difference in genotype distribution was observed between cases (Gly/Gly, 66.9%; Gly/Ser, 20.17%; Ser/Ser, 12.8%) and controls (Gly/Gly, 67.4%; Gly/Ser, 28.5%; Ser/Ser, 4.00%) (p = 0.013). The cases showed significantly higher frequency of the Ser allele compared to the controls (22.9% vs. 18.3%; OR: 1.32, CI: 0.95–1.83, p=0.013). The minor allele (Ser) showed a significant association with weight, BMI, fasting plasma glucose, total cholesterol level and LDLC had no effect on age, height, triglycerides, HDLC and leptin. In conclusion, Gly482Ser variant appears to be significantly associated with diabetes in Pakistani population. The variant appeared to exert its effect by changing serum fasting plasma glucose, total cholesterol and LDLC levels.