Introduction: Hypothyroidism is a condition with decreased levels of thyroid hormones and elevated levels of Thyroid stimulating Hormone. Hypercholesterolemia is the characteristic feature of hypothyroidism and is also predisposing factor of atherosclerosis. Cholesterol in the body is transported through lipoproteins called Low density lipoprotein (LDL) and High density lipoprotein (HDL). The ratios, LDL/HDL and total cholesterol/HDL reflectthe direction of transport of cholesterol and are conventionally used to assess risk of cardiovascular diseases. ApolipoproteinB (apo B)present in Very low density lipoprotein(VLDL), Intermediate density lipoprotein (IDL), and LDL; is considered as atherogenicwhereas apolipoproteinA1 (apoA1) present in HDL, is antiatherogenic, anti-inflammatory with antioxidative properties. ApoB/apoA1 ratio represents the balance of proatherogenic and antiatherogenic lipoproteins. So the case control study was carried out to know the effectiveness of this improved ratio in hypothyroidism. Objective: To find out levels of total cholesterol (TC), LDL, HDL, apoB,andapo A1 2) To find out ratios- LDL/HDL, TC/HDL and apoB/apoA1 3) To check the effectiveness of apoB/apoA1 ratio as marker of cardiovascular risk in hypothyroidism. Methodology: Group A consists of 30 clinically diagnosed and biochemically confirmed cases of hypothyroidism. The levels of TC, HDL estimated using the kit, LDL using Friedewald formula, apoB and apoA1 byimmuno-turbidimetricmethod and result were compared with Group B (n=30) age and sex matched controls. Results: The levels of TC, LDL, and apoB were found to be increased highly significantly (p__ampersandsignlt;0.001) and that of HDL and apoA1 decreased highly significantly (p__ampersandsignlt;0.001). A highly significant increase in ratios namely LDL/HDL, TC /HDL and apoB/apoA1 was also observed. Conclusion: It can be concluded from the present study that apoB/apoA1 ratio is comparable with LDL/HDL and TC/HDL ratios. ApoB/apoA1 ratio can be an improved marker for prediction of cardiovascular risk in hypothyroidism.