Irritable bowel syndrome (IBS) and gastroesophageal reflux disease (GERD) overlap. It is not clear whether GERD is caused by non‑erosive esophagitis, or erosive esophagitis. The Rome criteria are not widely used for the diagnosis of IBS in the clinic. In total, 1,489 IBS patients without red flags were included in the present retrospective study. They comprised of 1,331 females and 158 males with a mean age of 51 years. The diagnosis of IBS was verified by endoscopic and histopathological examinations. Whereas erosive esophagitis occurred in 97% of patients, only 66% had GERD symptoms. Endoscopy and histopathological examinations revealed that 1.4% of the IBS patients with diarrhea as the predominant symptom had other organic gastrointestinal diseases: 0.3% with celiac disease, 0.2% with Crohn's disease, 0.07% with ulcerative colitis, 0.6% with microscopic colitis, and 0.2% with colon cancer. Applying the Rome III criteria produced a sensitivity of 100% [95% confidence intervals (CI)=99.8‑100.0%] a specificity of 98.7% (95% CI=98.0‑99.2%), a positive likelihood ratio of 76.9%, and a negative likelihood ratio of 0%. IBS is associated with erosive esophagitis. Applying Rome III criteria without red flags and history, was effective in diagnosing IBS. Celiac disease and microscopic colitis should be considered as alternative diagnoses.