Objectives: To evaluate the adequacy of reporting of protocols for randomised trials on diseases of the digestive system registered in ClinicalTrials.gov and the consistency between primary outcomes, secondary outcomes and sample size specified in ClinicalTrials.gov and published trials. Design: Randomised phase III trials on adult patients with gastrointestinal diseases registered before January 2009 in ClinicalTrials.gov were eligible for inclusion. From ClinicalTrials.gov all data elements in the database required by the International Committee of Medical Journal Editors (ICMJE) member journals were extracted. The subsequent publications for registered trials were identified. For published trials, data concerning publication date, primary and secondary endpoint, sample size, and whether the journal adhered to ICMJE principles were extracted. Differences between primary and secondary outcomes, sample size and sample size calculations data in ClinicalTrials.gov and in the published paper were registered. Results: 105 trials were evaluated. Sixty-six trials (63%) were published. Thirty-one percent of trials were registered incorrectly after their completion date. Several data elements of the required ICMJE data list were not filled in, with lacking data in 22% and 11% of cases concerning the primary outcome measure and sample size. In 26% of the published papers data of sample size calculations were missing and discrepancies between sample size reporting in ClinicalTrials.gov and published trials existed. Conclusion: The quality of registration of randomised controlled trials still needs improvement.