This study compared heart-rate variability (HRV) indices of autonomic nervous system function during two nights of sleep between women with irritable bowel syndrome (IBS, n = 35) and healthy controls (n = 38), and among subgroups within the IBS sample based on predominant stool patterns. HRV measures were estimated in conjunction with polysomnographic sleep scoring to define sleep stage-specific autonomic indices. Overall, there were no differences in indicators of HRV between women with IBS and controls. However, within the IBS group, women with diarrhea-predominant IBS demonstrated significantly increased parasympathetic modulation and lower sympathetic/parasympathetic nervous system balance across sequential NREM periods and REM cycles compared to both constipation-predominant and alternating IBS subjects. These results suggest that differences in mean level of HRV between predominant bowel groups in IBS patients are large, and that this effect is consistent in the different sleep stages and at different times of night.