Aim: To evaluate treatment efficacy using objective quality criteria. Methods: A systematic review was performed of randomized controlled trials of endoscopically investigated dyspepsia (1979-2003) using the Jadad score and Rome II guidelines. The Jadad score differentiated studies as 'high quality' (score 4-5/5) vs. 'poor quality' (score 1-3/5). Three key Rome II guidelines on study design (cut-off of 0/3 or > 0/3) were also compared with the Jadad score. Results: Poor quality trials suggested a benefit of prokinetic therapy [relative risk (RR) of remaining dyspeptic, 0.47; 95% confidence interval (CI), 0.39-0.56), which was not confirmed in high quality trials (RR, 1.0; 95% CI, 0.84-1.19). There was a marked benefit of H-2-receptor antagonist therapy in poor quality trials (RR, 0.68; 95% CI, 0.61-0.76), but a marginal benefit in good quality trials (RR, 0.87; 95% CI, 0.79-0.97). Trial quality did not affect the small statistically significant benefit seen with Helicobacter pylori eradication. Two high quality trials suggested a limited benefit with the use of proton pump inhibitors, with no poor quality trials to provide a comparison. Separation of the studies by the Rome II criteria had a similar impact on the calculated treatment estimates. Conclusions: The magnitude of benefit of prokinetic and H-2-receptor antagonist therapies reported in previous meta-analyses has been over-estimated. The quality of trials has an impact on the efficacy estimates of treatment. The Rome II criteria for study methodology may be appropriate for judging study quality.