Abstract Background and study aims Irritable bowel syndrome (IBS), gastro-oesophageal reflux disease (GERD) and dyspepsia are three most important gastrointestinal disorders which occur frequently together in patients. This study aims to assess the association between IBS, GERD and dyspepsia by using loglinear model analysis. Patients and methods This cross-sectional household survey, the purpose of which was to find the prevalence of gastrointestinal symptoms, disorders and the related factors, has been done from May 2006 to December 2007 in Tehran province, Iran. Subjects were interviewed by trained personnel. GERD was diagnosed as the experience of heartburn and/or acid regurgitation at least once a week for the last 3months. IBS and dyspepsia were diagnosed according to the Rome III criteria. Loglinear models were applied to investigate the simultaneous association between IBS, GERD and dyspepsia. Results 77.9% of IBS patients had dyspepsia symptoms and 74.7% had GERD symptoms as well at the same time. As for the other two symptoms, 66% of GERD patients were also suffering from dyspepsia. Conclusions These three symptoms frequently overlap; the overlap is systematic and not by chance or random.