Type 2 Diabetes (T2D) and Hypertension are the major health issues affecting quality of life of young ages throughout the world, especially the third world countries facing more complications with diabetes due to poor disease management. The present study was conducted to explore the association of genetic polymorphism with T2D and hypertension in the Punjabi population. The case control study was conducted comprising of 288 patients (118 male, 170 female) and 170 controls (104 male, 66 female). The selected genes along SNPs were NPPA (rs5064 G>A, rs5063 C>T) and IL6 (rs1800796 C>G). DNA was amplified by Nested PCR and sequencing was performed for genotyping. The rs5063 and rs5064 from NPPA was not associated with hypertension and not involved in the predisposition of diabetes (p < 0.05). Moreover, rs1800796 (IL6) showed an association (p < 0.001) with diabetes (OR = 0.394 (0.265, 0.584). SNPs analysis with demographic data confirmed that rs1800796-CC (p = 0.008) is significantly associated with positive family history of T2D. Risk of T2D development associated with IL6 was confirmed, whereas NPPA was not associated with hypertension.