This study evaluated changes of lipids and lipoprotein (a) [Lp (a)] as atherosclerotic risk factors and the effects of levothyroxine (LT4) treatment oil these parameters in patient with subclinical hypothyroidism (SH), defined by increased concentrations of thyrotropin (TSH) and normal thyroid hormone concentrations. We prospectively included 35 female patients with SH and 30 healthy controls. Serum lipid measurements and clinical score as well as fT3, fT4, and TSH levels were assessed at baseline. Body mass index (BMI) was also calculated. Women with proven SH received LT4 treatment that continued for 6 months. Twenty-six of 35 patients completed the study. At the end of treatment period, the same parameters were determined. Total cholesterol was significantly increased in patients with SH when compared with those of controls (p < 0.01), but increase of LDL-cholesterol (LDL-C) and Lp (a) were not significant (p > 0.05). In the levothyroxine-treated group, total cholesterol and LDL-C were significantly reduced when compared with the baseline values of women with SH (p < 0.05). Zulewski clinical score assessing symptoms and signs of hypothyroidism improved significantly with treatment (p < 0.001). In conclusion, serum lipids as important atherosclerotic risk factors increased before treatment and decreased with treatment. Levothyroxine, therapy is effective in SH and improvements in serum lipids suggests that LT4 treatment also decreases the risk of atherosclerotic diseases.