Subclinical hypothyroidism is one of the most common endocrine disorders in India. As thyroid hormones have effect on lipid metabolism, subclinical hypothyroidism may lead to significant dyslipidemia. Dyslipidemia is a major risk factor for atherosclerosis and ischemia heart disease. This study was done to see the levels of serum Apolipoprotein A1 (Apo A1) and HDL cholesterol levels among subclinical hypothyroid patients and healthy euthyroid controls. Study involved 35 subclinical hypothyroid cases and 35 age & sex matched healthy euthyroid controls. Serum Apo A1 and HDL cholesterol levels were measured by commercially available kits. Statistical analysis was done with Students’t- test and Pearson correlation using SPSS 17.0. Serum Apo A1 and HDL cholesterol were significantly low in subclinical hypothyroid cases compared with controls (p<0.001). Serum Apo A1 and HDL cholesterol were significantly negatively correlated with serum TSH levels (p<0.05).This study suggests that, serum Apo A1 and HDL cholesterol levels are significantly reduced in subclinical hypothyroidism patients. As these dyslipidemic changes are strongly associated with occurrence of ischemic and metabolic diseases, it is beneficial to timely detect and control dyslipidemia in such patients.