AIM: To investigate the association of gastroesophageal reflux disease (GERD) and irritable bowel syndrome (IBS) in Iranian patients and examine the prevalence of functional symptoms of the gastrointestinal tract in patients presenting with either IBS, GERD or both. METHODS: Six thousand four hundred and seventy six patients presented to the Gastro-intestinal (GI) clinic with symptoms of functional dysfunction of GI tract, 1419 patients (62.0% women, 38.0% men; mean age: 37.4 +/- 11.5 years) met Rome II or Rome III criteria (depending on the year of diagnosis) for IBS. 2658 patients were diagnosed with GERD based on clinical presentation and endoscopic findings. We assessed other functional symptoms (epigastric pain, nausea, vomiting, belching, constipation and diarrhea) in patients suffering from GERD, IBS or both. RESULTS: Among IBS subjects, 63.6% (69.0% women, 31.0% men; mean age: 36.4 +/- 10.3 years) also had GERD, whereas 34.7% of the non-IBS patients had GERD [odds ratio (OR) = 3.2, 95% confidence interval (CI): 2.9-3.7, P < 0.0001]. Among patients with GERD, 33.9% of subjects met Rome criteria compared to 13.5% of non-GERD patients (OR = 3.6, 95% CI: 3.1-4.3, P < 0.0001). Prevalence of all functional symptoms was higher in overlapping GERD and IBS subjects, when compared with their prevalence in the IBS subjects without GERD or GERD only subjects (P < 0.05). CONCLUSION: This finding shows that in overlapping GERD and IBS, other functional abnormalities of the GI tract are also highly prevalent, suggesting a common underlying dysfunction.