To determine the relationship between sub-clinical thyroid dysfunction (STD) and dyslipidemia. Methodology: This cross sectional study was conducted in Pakistan Health Research Centre (PHRC), Khyber Medical College and Khyber Medical University, Hayatabad Peshawar, Pakistan in the year 2012-2013. Thirty patients of both genders and between 10-70 years of age, residing in Peshawar were studied. Lipid profiles were assessed for relationship with sub-clinical hypothyroidism (SCH-I) and sub-clinical hyperthyroidisms (SCH-I). Results: Total cholesterol (TC) was 194.67 ±34.81 in (SCH-I) and 151.29 ±35.22 in (SCH-II); low density lipoprotein cholesterol (LDL-C) was 146.56 ±47.6 in (SCH-I) and 89.48 ±27.15 in (SCH-II); triglycerides (TG) were 91.89 ±33.62 in (SCH-I) and 125.62 ±68.98 in (SCH-II). Serum TC and LDL-C levels were significantly high in SCH-I (p values 0.033 & 0.029 respectively). Serum TC, LDL-C, VLDL-C and TG levels were negatively correlated with STD (r values -0.601, -0.533, -0.401 & -0.401 respectively). Conclusions: Serum TC and LDL-C levels were high in SCH-I. Lipid profile was non-significant in SCH-II patients. Serum TC, LDL-C, VLDL-C and TG were negatively correlated with STD.