The timing of circadian oscillators cannot be measured directly in humans and indirect measures such as the secretory profiles of hormones, body temperature and EEG sleep recordings must suffice instead. External and internal factors called masking can influence the apperent circadian rhythms in these variables without affecting the biological clock or clocks. In our present study, we have been comparing the circadian system of depressed patients and normal controls under routine ward conditions and then repeating these measurements in conditions where the internal and external sources of masking have been controlled by holding diet, activity, posture, lighting and wakefulness constant. Preliminary data of the temperature rhythm in patients with affective disorders confirm that mean body temperature is increased in both depression and mania compared to controls and the timing, or phase of the temperature is shifted to an abnormally early time in both phases of the illness. The disturbances in temperature cannot be attributed to masking since they persist under constant conditions. Consistent with our previous observations made in a group of rapid-cycling manic depressives, patients with major depression show a decreased nocturnal rise in TSH and diminished TSH response to sleep deprivation. The disturbance in temperature regulation in association with abnormal hypothalamic-pituitary-thyroid function may be indicative of an underlying disorder of metabolism in patients with major depression.