Klinefelter syndrome has been associated with thyroid abnormalities, the genesis of which is not yet fully clear. The aim of this study was to evaluate thyroid function in Klinefelter syndrome subjects during the pubertal period. Chemiluminescent microparticle immunoassay was used to analyze Thyroid-Stimulating Hormone, fT3 and fT4 concentration in serum samples from 40 Klinefelter syndrome pubertal boys with classic 47,XXY karyotype and 157 healthy age-matched controls. 13 Klinefelter syndrome patients also underwent Thyrotropin-Releasing Hormone testing to evaluate hypothalamic-pituitary function. fT3 levels were significantly lower in Klinefelter syndrome patients than in age-matched controls (p < 0.001). No significant differences were found for Thyroid-Stimulating Hormone (p = 0.138) or fT4 (p = 0.274), but the serum levels of Klinefelter syndrome patients tended to cluster around the lower part of the reference range for the assay. Three of the thirteen Klinefelter syndrome patients undergoing the Thyrotropin-Releasing Hormone test had an adequate response, one had a prolonged response at 60 min and nine responded inadequately. This study demonstrated for the first time that pubertal Klinefelter syndrome patients have significantly lower fT3 serum levels than do healthy age-matched boys, whereas Thyroid-Stimulating Hormone and fT4 are normal, albeit at the lower end of the reference range. Most patients showed an inadequate/prolonged response to pituitary stimulation with Thyrotropin-Releasing Hormone. These findings suggest a combined form of both central and peripheral hypothyroidism in Klinefelter syndrome boys during pubertal development.