Symptoms consistent with hypothyroidism or adrenal insufficiency, such as lethargy, anorexia, cold intolerance, weakness, hypotension or paraesthesia, are frequently reported in the literature in patients with Human African Trypanosomiasis (HAT), but an endocrine origin for these symptoms has not yet been demonstrated. Thyroid and adrenocortical function were assessed in 60 patients with late-stage HAT and compared to those in 60 age- and gender-matched healthy controls. Clinical assessment and endocrine laboratory examinations were performed on admission, within 2 days after the end of treatment and at follow-up 3 months later. Signs and symptoms of hypothyroidism, such as fatigue, cold sensation, constipation, paraesthesia, peripheral oedema and dry skin, were significantly more frequent in HAT patients than in the controls. However, these signs and symptoms could not be attributed to hypothyroidism due to the lack of supporting laboratory data, and thus empirical replacement therapy for the clinically suspected hypothyroidism was not warranted. Signs and symptoms consistent with adrenal insufficiency, such as weakness, anorexia, weight loss or hypotension, were significantly more frequent in HAT patients than in controls, but they could not be associated with an insufficiency of the adrenocortical axis. Higher basal levels of cortisol were found in HAT patients than in controls, which can be viewed as a stress response to the infection. However, a transitory adrenal insufficiency was suspected in 8% of HAT patients at admission and in 9% at discharge. All values were normal at follow-up 3 months later.