BACKGROUND: The prevalence of coeliac disease (CD) may be increased in individuals with dyspepsia, but evidence is conflicting. AIMS: To conduct a systematic review and meta-analysis of studies reporting prevalence of CD in dyspepsia. METHODS: MEDLINE, EMBASE, and CINAHL were searched up to February 2009. Case series and case-control studies applying serological tests and/or distal duodenal biopsy for CD to unselected adults with dyspepsia were eligible. Prevalence of positive coeliac serology and biopsy-proven CD were pooled for all studies and compared between cases and controls using an odds ratio (OR) and 95% confidence interval (CI). RESULTS: Fifteen studies were identified. Prevalence of positive coeliac serology was higher in cases with dyspepsia (7.9%) compared with controls (3.9%), but not significantly so (OR for positive endomysial antibodies or tissue transglutaminase 1.89; 95% CI 0.90-3.99). Prevalence of biopsy-proven CD following positive serology was also higher (3.2% in cases vs. 1.3% in controls), but again this was not statistically significant (OR 2.85; 95% CI 0.60-13.38). Prevalence of biopsy-proven CD was 1% in ten studies performing duodenal biopsy first-line. CONCLUSION: Prevalence of biopsy-proven CD in subjects with dyspepsia was 1% and was higher than in controls, although this difference was not statistically significant.