Background Sleep disturbances and changes in self-reported discomfort and melatonin secretion are common in the post-operative period. We aimed to study the distribution of sleep stages in the perioperative period and evaluate changes in secretion of the melatonin metabolite aMT6s and subjective parameters of sleepiness, pain, general well-being and fatigue in patients undergoing surgery for breast cancer. Methods Twelve patients, 30-70 years, undergoing lumpectomy were included. Polysomnography was performed the night before surgery (PREOP), the night after (PO1) and 14 days after (PO14). Recordings were scored as awake, light-sleep, slow-wave sleep and rapid-eye-movement (REM) sleep. Sleep stages were analysed as % of total sleep time (TST). Self-reported discomfort was assessed using questions about the level of fatigue, well-being, pain and sleepiness. Urinary aMT6s was measured by radioimmunoassay. Results There was significantly decreased REM sleep on PO1 (5.9% of TST) compared with PREOP (18.7% of TST) (P < 0.005). An increase in light sleep was observed on PO1 (68.4% of TST) compared with PREOP (55.0% of TST) (P < 0.05). No significant changes in TST, sleep latency, sleep period or total time awake were found. The observed sleep changes were normalised after 2 weeks. No significant changes were found in pain, well-being, fatigue or sleepiness. Night secretion of aMT6s showed a trend towards a decrease from PREOP to PO1 (P = 0.09) and normalisation on PO14 (P = 0.27 between PREOP and PO14). Conclusion Patients with breast cancer undergoing lumpectomy had significantly disturbed sleep architecture the night after surgery, and these changes were normalised after 2 weeks.