Objective To systematically evaluate the effectiveness and safety of itopride vs. mosapride in patients with functional dyspepsia, so as to provide references for clinical practice. Methods According to strict inclusive and exclusive criteria, relevant randomized controlled trials (RCTs) on itopride vs. mosapride for functional dyspepsia were searched in CENTRAL, Medline, Embase, ISI, OVID, CBM, VIP, WanFang Data and CNKI from the date of their establishment to November 2011. Two reviewers independently screened literature, extracted data and evaluated methodological quality. Meta-analyses were conducted using Revman 5.1 software. Results A total of 4 trials involving 363 patients were included and data were coped with meta-analysis. a) About the improvement of overall symptoms: itopride was not superior to mosapride, with no significant difference (OR=1.62, 95%CI 0.53 to 4.93, P=0.4); b) About the improvement of single symptom: itopride was not superior to mosapride in improving single symptom as follows: postprandial fullness, upper abdominal distention, poor appetite, and upper abdominal pain, with no significant difference; and c) About the incidence of adverse events: itopride was similar to mosapride (OR=0.63, 95%CI 0.31 to 1.29, P=0.21). Conclusion Current evidence shows that itopride is similar to mosapride in effectively improving overall symptoms and single symptom, and it has fewer side effects than mosapride does. Due to the low quality of most included studies, more strictly-designed and large-scale RCTs are needed to provide reasonable proofs for clinic.