The Rome III criteria classify patients complaining of constipation into two main groups: patients with functional constipation (FC) and patients with constipation predominant irritable bowel syndrome (IBS-C). The purpose of this study was to identify differences in the intensity of symptoms and total and segmental colonic transit time in these two types of patients. We performed a prospective evaluation of 337 outpatients consecutively referred for chronic constipation and classified according to the Rome III criteria as FC or IBS-C. They were asked to report symptom intensity, on a 10-point Likert scale, for diarrhea, constipation, bloating and abdominal pain. Stool form was reported using the Bristol scale, and colonic transit time was measured by using multiple-ingestion single-marker single-film technique. Statistical analysis was completed by a discriminant analysis. Female gender and obstructed defecation was more frequent in IBS-C patients than in FC patients. IBS-C patients reported greater symptom intensity than FC patients, but stool form, and total and segmental colonic transit time were not different between the two groups. Multivariate logistic regression showed that only two parameters, bloating and abdominal pain, were related to the IBS-C or to the FC phenotype, and discriminant analysis showed that these two parameters were sufficient to give a correct classification of 71% of the patients. Our study suggests that self-evaluation of abdominal pain and bloating is more helpful than colonic transit time in classifying patient as IBSaEuroC or FC.