A diverse range of conditions share symptoms commonly identified with irritable bowel syndrome. The objective of this study was to examine the diagnostic process in identifying additional diagnoses in women who are attending a clinic for evaluation of symptoms suggestive of irritable bowel syndrome. A retrospective audit was conducted of anonymous data gathered on consecutive female patients presenting to a specialist nurse-led service in Christchurch, New Zealand, with a provisional diagnosis of irritable bowel syndrome. A protocol containing routine pathology investigations and physical examination was used. Alarm features were identified and pertinent investigations were implemented. Rectocele was detected on rectal examination. Final diagnosis was noted and compared with baseline symptom data. Of 231 patients, 187 initially met Rome III criteria for irritable bowel syndrome. Red flags and abnormal investigations led to an alternate diagnosis in a further 27 patients. Of the 160 patients with irritable bowel syndrome, 31% were found to have a rectocele. They were seven times more likely to report a symptom associated with pelvic floor dysfunction (p <.0001) and four times more likely to report constipation (p =.0003). The use of a protocol including routine investigations and physical examination improves diagnostic yield. Pelvic floor dysfunction should be considered in those with unique symptom patterns and rectocele in the setting of irritable bowel syndrome.