Circadian rhythms for cortisol, 6-sulphatoxy melatonin and core body temperature were compared in control subjects and patients with functional abdominal pain. There were 20 patients with biliary pain after cholecystectomy, ten with biliary pain without cholecystectomy and 14 with irritable bowel syndrome. Rhythms were determined by urine collections at intervals of 4 h for 48 h and by overnight monitoring of core body temperature using the Vitalog system. Data were fitted to a sine curve to yield the time of maximal urinary excretion/lowest temperature and the amplitude of each rhythm. Urinary excretion of free cortisol was similar in patients and control subjects. For urinary 6-sulphatoxy melatonin, the timing (phase) of rhythms was similar in patients and controls but those with pain had a lower urinary excretion of 6-sulphatoxy melatonin (p less than 0.05) and a rhythm of lower amplitude (p less than 0.02). The amplitude of the temperature rhythm was also lower in patients with biliary pain with and without prior cholecystectomy (p less than 0.05). Functional abdominal pain is associated with 6-sulphatoxy melatonin and temperature rhythms of low amplitude, presumably because of suppression of circadian oscillators.