Objective: The lack of overt signs and symptoms and controversies surrounding the thyroid stimulating hormone (TSH) reference range variability make the management of subclinical hypothyroidism (sHT) a challenge. Because muscle cramps and weakness have been noted in sHT, histological skeletal muscle examination may be of diagnostic significance as the presence of abnormalities would substantiate a significant consequence of the mild thyroid failure presumed to be present in the individual with sHT. The objective of this study was to investigate the ultrastructural and histological changes of skeletal muscle associated with sHT. Design: Skeletal muscle biopsies from the vastus lateralis were obtained from four subjects with sHT. Samples were fixed, sectioned, and stained for quantitative and qualitative electron and light microscopic analysis. Main Outcome: Analyses revealed characterizable morphological and ultrastructural alterations and quantitative mitochondrial variations between subjects, indicative of skeletal muscle mitochondrial dysfunction in sHT patients. For the 4 subjects, mean mitochondrial perimeter (MP) was 1.09 ± 0.312 ì, mean mitochondrial area (MA) was 0.10 ± 0.05 ì2, and mean mitochondrial volume density was 1.92 ± 0.95. Conclusions: The observed and quantified mitochondrial alterations and the noted morphological and ultrastructural alterations identify previously undocumented pathological skeletal muscle alterations associated with sHT. The observed morphological and ultrastructural alterations lend support to a trend of progression of sHT into overt hypothyroidism as a result of mitochondrial dysfunction and associated metabolic shift. The identification of these skeletal muscle alterations as sequelae of sHT may lend convincing objective evidence of a pathophysiologically significant abnormality in patients with sHT. If so, this should diminish the substantial resistance to treatment of these patients at an early stage of disease and attenuate the progression to overt hypothyroidism.