Relations between thyroid function and lipids remain incompletely understood. Our objective was to determine whether lipoprotein subparticle concentrations are associated with thyroid status. We conducted a prospective clinical study and cross-sectional cohort analysis at a university endocrine clinic and the Framingham Heart Study. Subjects included 28 thyroidectomized patients with short-term overt hypothyroidism and 2944 Framingham Offspring cohort participants. Fasting subclass concentrations of very-low-density lipoprotein (VLDL), intermediate-density lipoprotein, low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) particles were measured by nuclear magnetic resonance spectroscopy. TSH values were also measured. Total cholesterol and LDL-C were increased during short-term overt hypothyroidism. Large LDL subparticle concentrations increased during hypothyroidism (917+/-294 vs. 491+/-183 nmol/liter; P<0.001), but more atherogenic small LDL was unchanged. Triglycerides marginally increased during hypothyroidism, small VLDL particles significantly increased (P<0.001), whereas more atherogenic large VLDL was unchanged. Total HDL-C increased during hypothyroidism (76+/-13 mg/dl vs. 58+/-15 mg/dl; P<0.001). There was no change in large HDL-C particle concentrations, whereas small (P<0.001) and medium (P=0.002) HDL-C particle concentrations decreased. Among Framingham women, adjusted total cholesterol and LDL-C were positively related to TSH categories (P<or=0.003). This was due to a positive correlation between adjusted large LDL subparticle concentrations and log-TSH (P<0.0001); log small LDL subparticle concentrations decreased slightly as log-TSH increased (P=0.045). Among Framingham men, the only significant association was a positive association between log-TSH and log large HDL subparticle concentrations (P=0.04). There is a shift toward less atherogenic large LDL, small VLDL, and large HDL subparticle sizes in hypothyroid women.