Our aim was to study autonomic function in patients with Irritable bowel syndrome (IBS) without constipation and psychiatric comorbidity. Respiratory sinus arrhythmia (RSA) (representing cardiac vagal activity), skin conductance (representing sympathetic activity) and heart rate were measured at baseline and as a response to emotional stress and rectal discomfort in 33 women with IBS and 21 healthy women. Baseline heart rate was higher in the patients than in the healthy volunteers. Both groups had decreased RSA and increased heart rate and skin conductance level when exposed to emotional stress, but the autonomic responses did not differ significantly between the groups. At discomfort threshold the patients had increased heart rate response and skin conductance amplitude when compared to the healthy volunteers. Correlations between autonomic responses and the depression subscale of the Hospital Anxiety and Depression (HAD) score differed markedly between the diarrhea-predominant IBS patients and the IBS patients with alternating stool habits.