The aim of this study was to investigate whether dysfunction of the thyroid axis is related to clinical characteristics in major depression. Thyrotropin (TSH) responses to 8 AM and 11 PM protirelin challenges (TRH, 200 μg IV) were examined, on the same day, in 108 drug-free DSM-IV euthyroid major depressed inpatients. Twenty six patients had a single major depressive episode; the remaining 82 patients were classified according to the course of recurrent episodes: 53 with full interepisode recovery, 29 without full interepisode recovery. Based on their TRH-TSH test responses, patients were also classified according to stage of thyroid axis dysfunction (i.e. stage 1: blunted ΔΔTSH alone [i.e. abnormally low difference between 11 PM-ΔTSH and 8 AM-ΔTSH]; stage 2: combination of blunted ΔΔTSH and 11 PM-ΔTSH; stage 3: combination of blunted ΔΔTSH, 11 PM-ΔTSH and 8 AM-ΔTSH). The degree of thyroid dysfunction was moderate in patients with a single major depressive episode (no thyroid dysfunction: 35%; stage 1: 35%; stage 2: 27%; stage 3: 3%); intermediate in patients with full interepisode recovery (no thyroid dysfunction: 21%; stage 1: 45%; stage 2: 19%; stage 3: 15%); and marked in patients without full interepisode recovery (no thyroid dysfunction: 3%; stage 1: 24%; stage 2: 27%; stage 3: 46%) (χ2 = 22.8, df = 6, p = 0.0008). These differences could not be explained by differences in age, gender distribution, or severity or subtype of depression. Our results suggest that level of thyroid axis dysfunction is related to longitudinal course of depression.