OBJECTIVES: With availability of several colorectal cancer screening tools, the cost-effectiveness of population-based screening programmes is of interest. The goal of this study was to estimate the per-procedure cost of conventional colonoscopy (COL) and flexible sigmoidoscopy (SIG) in an outpatient endoscopy clinic. METHODS: An activity based costing approach was carried out using time-and-motion techniques on 104 COL and 48 SIG procedures performed in St. Paul's Hospital (SPH) between July and October 2004. Observation began with patient registration in the clinic and ended with patient discharge. Direct costs, including nursing and physician time, supplies and medications, were estimated. Indirect costs included physician and pathology fees, scope repair and cleaning expenses. Hospital overhead costs were determined through SPH finance department. Total cost was calculated as the sum of direct, indirect and overhead costs. Student's t-tests were performed to determine any significant differences (P<0.10) of mean total cost between groups derived from baseline variables. Linear regression analysis of cost was also conducted. All costs are reported in 2004 Canadian dollars. RESULTS: Mean age of patients was 56 (22; 88) years for COL and 51 (17; 90) years for SIG. Mean total time was 189 (106; 317) minutes for COL and 53 (14; 111) minutes for SIG. Mean procedure time for COL and SIG was 34 (18; 61) minutes and 14 (7; 35) minutes, respectively. Total cost was $522 ($360; $679) for COL and $176 ($105; $287) for SIG. Physician and pathology fees accounted for 61% of total cost for COL and 58% for FSIG. Number of biopsies and total time have significant predictive power on total cost for both procedures. Sex and number of polypectomies are significant for COL. CONCLUSIONS: Detailed costing of such procedures provide useful estimates of health resource use which can be applied in economic evaluations of CRC screening.