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Background: Colonoscopy is a valuable tool for diagnosing various colonic pathologies. There is little recent research regarding the use of colonoscopy in South Africa. Objective: To describe the findings of the audit done on the practice of colonoscopy in a specialised gastroenterology unit (GEU) of a tertiary teaching hospital. Design: A retrospective audit of colonoscopies performed between the 01 January 2008 and 31 March 2010 in a single gastroenterology unit at Charlotte Maxeke Johannesburg Academic Hospital(CMJAH) was conducted. Details of colonoscopy records were obtained from an administrative database of patient files. No patient specific inclusion or exclusion criteria were applied. Results: In total 1143 colonoscopies were performed during the study period, and 989 were analysed. The mean age was 63.04 years (10 - 93), 61.58% female, 61.48% were Caucasians and 25.88% were of black ethnicity. The indications for colonoscopies were; screening for colorectal cancer (22.95%), case findings (14.16%) and surveillance (14.96%). Caecal intubation rate (CIR) was 80.08%. Findings included macroscopically normal colons (38.12%), polyps (28.18%) and diverticular disease (23.15%). Of the biopsies obtained during colonoscopy procedures 30.50% were reported as normal colonic mucosa, 10.40% revealed adenocarcinoma and 55.37% were tubular adenomas. Conclusions: The audit identified a number of shortfalls, which include: poor colonoscopy performance quality as reflected by the low CIR, non standardised colonoscopy reporting format resulting in paucity of information on scope reports, underrepresentation of the black community, to mention a few. It therefore would appear, based on the findings from this study that there is room for improvement in a number of areas in the practice of colonoscopy in this unit. Further studies may be of value to identify reasons behind these shortfalls. [ABSTRACT FROM AUTHOR]