Chronic kidney disease (CKD) patients have higher HOMA-IR index compared to otherwise healthy metabolic syndrome controls. The aim of this work was to compare the biochemical profile, symptoms and signs of Metabolic Syndrome (MS), between chronic kidney disease patients and non-chronic kidney disease metabolic syndrome subjects, using the World Health Organization criteria. it is a case-control study. Among the CKD patients, 20 patients fulfilling the criteria for metabolic syndrome were included in the study and compared with the age, sex matched otherwise healthy metabolic syndrome subjects. Individuals aged >18 yrs and above were included in the study. Fasting glucose, anthropometric measurements, lipid estimations, and biochemical parameters were done in all the participants, who fulfilled the WHO criteria of metabolic syndrome. All the cases belonged to stages 3 & 4 of CKD. Presence of symptoms among cases were due to their CKD condition, waist hip ratio (W/H) ratio is significantly higher in cases than controls (P<0.05). Both systolic as well as diastolic blood pressure is higher in cases (M 142±19.6, F141 ± 11.3).There was significant difference in the HDL and LDL level among cases and controls HDL level being higher in females among cases(F 46.5±8.31) , whereas LDL level was higher in females among controls (F111.3±55.9). Fasting insulin level was significantly lower among cases in both females and males (Case; M 42.6±8.3, F32.04+14.4; Controls; M56.5±6.6, F 57.5±9.4) similarly HOMA-IR values were significantly lower in cases than controls (Case M7.9±0.86, F7.4±3.7, Controls M13.4±3.5 F12.1±3.4).None of the comparative studies, between CKD and otherwise healthy metabolic syndrome cases have reported higher HOMA-IR levels in controls than CKD patients. HSCrp level was higher in cases than controls (case M 9.3±9.6 F5.9±7.2; Controls M2.5±3.2, F1.9±2.4). Sodium and Potassium levels were significantly higher in cases than controls. Calcium levels were higher in controls than cases, alkaline phosphatase is significantly higher in cases than controls. Though both the cases and controls, are insulin resistant, there is significant difference between HOMA –IR index among cases and controls, HOMA-IR value is higher among controls than CKD patients.