The objective of this study was to determine how depressive symptoms affect autonomic activity during sleep, objective and subjective sleep, and gastrointestinal symptom severity in women with irritable bowel syndrome (IBS). Seventy women who met the Rome II criteria for IBS and 21 healthy volunteers participated. All participants were recruited from the surrounding community. IBS patients were stratified into two groups based on their Beck Depression Inventory II score and 44 IBS patients with depressive symptoms (IBS+DS) were compared to 26 IBS patients without depressive symptoms (IBS-DS). Autonomic activity was measured by heart rate variability (HRV) analysis. Fifteen-minute segments were selected from a baseline presleep period, stage 2, slow-wave sleep, and rapid-eye movement sleep for heart rate variability spectral analysis. Subjective sleep quality was assessed by the Pittsburg Sleep Quality Index (PSQI) and gastrointestinal symptom severity was assessed by an 18-item questionnaire. The IBS+DS group reported significantly (P < 0.01) more sleep complaints, measured by the PSQI, than the IBS-DS group and healthy controls. The IBS+DS group took significantly (P < 0.05) longer to enter their first rapid-eye movement period than healthy controls. The IBS+DS group reported significantly (P = 0.01) increased gastrointestinal symptom severity compared to the IBS-DS group. There were no significant group differences in autonomic activity during the baseline presleep period or sleep stages. The results demonstrated that IBS patients with significant depressive symptoms had increased gastrointestinal symptom severity, increased sleep complaints, and alterations in sleep architecture compared to healthy controls and IBS patients without significant depressive symptoms.