Thyrotropin levels are outside normal reference range in subclinical thyroid disease. Metabolic syndrome (MetS) involves clustered cardiovascular risk factors, including abnormal lipids, insulin resistance, and hypertension. This study aimed to investigate associations between subclinical thyroid disease, thyrotropin levels, and metabolic syndrome in healthy subjects and identify associated biochemical markers. This cross-sectional study evaluated 9,055 healthy subjects examined at the Health Management Center, National Taiwan University Hospital from January 1, 2009 to December 31, 2009. Data collected included age, sex, height, weight, body mass index, waist circumference, pulse rate, and systolic/diastolic blood pressure. History of pregnancy, smoking/drinking status, family/personal thyroid disease, diabetes, dyslipidemia, and hypertension was obtained. Laboratory data included thyroid function tests, fasting glucose level, lipid profile, and C-reactive protein level. Participants were classified into subclinical hypothyroidism, subclinical hyperthyroidism, and euthyroid groups according to thyrotropin levels. In euglycemic subjects, thyroid-stimulating hormone (TSH) levels correlated positively with waist circumference, triglycerides (TG), non-high density lipoprotein (HDL) cholesterol, diastolic blood pressure. In subclinical hyperthyroid subjects, TSH levels correlated positively with low density lipoprotein cholesterol (LDL-C), non-HDL cholesterol. No significant correlations were found between TSH levels and variables in the subclinical hypothyroid group. In the entire study population, TSH levels correlated positively with TG, non-HDL cholesterol, and systolic blood pressure (SBP)/diastolic blood pressure (DBP), but no correlation was shown with HDL-C. No significant associations were seen between MetS prevalence and thyrotropin levels. No clinically relevant biochemical markers, differences in thyrotropin levels, or statistical correlations are shown between subclinical thyroid disease and metabolic syndrome in healthy individuals.