Aims: Computerized reporting systems that generate standardized endoscopy reports are available and facilitate easy retrieval of data for quality assurance review. We aim to compare the accuracy of extracted database fields in our reporting system (endoPRO) for key measures of quality to the final edited endoscopy report for colonoscopy procedures. Methods: In a retrospective analysis, we compared data retrieved from endoPRO to the final colonoscopy reports at Hamilton Health Sciences (HHS). The data included demographics, indications for procedures, bowel prep quality, findings, extent of exam, and recommendations. Discrepancies, changes or missing information pertaining to key quality indicators for colonoscopies were recorded. Results: In total, 1843 colonoscopy procedures were done at HHS from January to March 2010, and reports for 592 colonoscopies, randomly selected, were analyzed for this study. Discrepancies were seen in: Indication – 34 cases (5.7%), Assistants present during colonoscopy – 94 cases (15.9%), Quality of bowel preparation – 35 cases (5.9%), Findings & impressions – 38 cases (6.4%) including polyps, inflammation, diverticulosis and haemorrhoids. Conclusions: Our study demonstrates the variability between data found in patients’ final colonoscopy reports and data retrieved from the endoscopy databases. Structured endoscopy reporting and the use of databases facilitate quality assurance but editing of procedure reports after structured data entry compromises accuracy of the data in key quality measures. Inaccurate or incomplete data recording will compromise the enhancements in quality assurance that would accrue otherwise from regular audit processes.