Background Dyspepsia and irritable bowel syndrome (IBS) are common in Western populations. Aim To determine the epidemiology of dyspepsia and IBS in China. Methods A representative sample of 18 000 adults from five regions of China were asked to complete the modified Rome II questionnaire; 20% were asked to complete the 36-item Short Form Health Survey (SF-36). Participants from Shanghai were invited to provide blood samples and undergo oesophagogastroduodenoscopy. Odds ratios (ORs) and 95% confidence intervals (CIs) were determined using a multivariate logistic regression model. Results The survey was completed by 16 091 individuals (response rate: 89.4%). Overall, 387 participants (2.4%) had dyspepsia and 735 (4.6%) had IBS. All SF-36 dimension scores were at least five points lower in individuals with than without dyspepsia or IBS (P ≤ 0.001). In Shanghai, 1030 (32.7%) of the 3153 respondents agreed to endoscopy; neither dyspepsia nor IBS was found to be associated with reflux oesophagitis, peptic ulcer disease or Helicobacter pylori infection. Conclusions Prevalence estimates for dyspepsia and IBS in China are lower than in Western populations. In China, dyspepsia or IBS symptoms are generally not associated with underlying organic disease. © 2010 Blackwell Publishing Ltd.