Background: The role of Hyperhomocysteinemia (HHomocysteine) as a risk factor for atherosclerosis in Chronic kidney disease (CKD) has gained much interest worldwide. The primary objective of the study was to ascertain the association between serum homocysteine levels and GFR. Method: This case control study was done in stage 3,4 and 5 of CKD (cases= 63, controls =21) to assess the association between Serum homocysteine (S.Homocysteine), Serum creatinine (S.Cr), Glomerular Filtration Rate(GFR) and Carotid intima media thickness (CIMT). Result: Statistical analysis using ANOVA and pearsons correlation revealed a significant association between S.Homo-cysteine and stages of CKD (p=0.00), S.Homocysteine and GFR (p=0.00, rsq=0.3686) S.Homocysteine and CIMT (p=0.002, rsq=0.1429) and CIMT and CKD (p=0.00). Conclusion:On the basis of these observations, it was concluded that HHomocysteine exists in CKD and that it produces atherosclerosis. Hence early screening and treatment for HHomocysteine and atherosclerosis should be done in CKD to prevent cardiovascular diseases.