Background Chronic sleep deprivation combined with work during the night is known to affect performance and compromise residents' own safety. The aim of this study was to examine markers of circadian rhythm and the sleep-wake cycle in surgeons working night shifts. Methods Surgeons were monitored prospectively for 4 days: pre call, on call, post call day 1 (PC1), and post call day 2 (PC2). The urinary metabolite of melatonin and cortisol in saliva were measured to assess the circadian rhythm. Sleep and activity were measured by actigraphy. Subjective measures were assessed by the Karolinska Sleepiness Scale and Visual Analog Scale of fatigue, general well-being, and sleep quality. Results For both metabolite of melatonin and cortisol, a significant difference (P <.05) was found in the measurement period between on call and pre call values. There was increased sleep time during the day on call and on PC1. For all subjective measures, a marked deterioration was seen on PC1. Conclusion Surgeons' circadian rhythm was affected by working night shifts.