OBJECTIVE: The potential effect of CT colonography (CTC) on endoscopic colonoscopy (EC) has been the topic of much speculation. The aim of this study was to evaluate the impact of a CTC screening program on colonoscopy in clinical practice. METHODS: At our institution a third-party reimbursed CTC colorectal cancer (CRC) screening program was established in 2004. The number of CTC monthly exams performed, monthly EC total and screening exams performed, EC with polypectomy performed, and the number of referrals for EC screening exams requested were prospectively examined in the first 33 months after introduction of a CTC CRC screening program. RESULTS: The mean number of overall (378.5 vs 413.1) and screening (150.7 vs 162.9) colonoscopy exams performed per month did not change significantly after screening CTC was introduced. The mean number of monthly CTC exams performed rose significantly throughout the first year of the study from 39 initially to a peak of 147.6 cases per month but decreased slightly to 114.3 monthly exams at the end of 2006. A mean 10.0 patients per month were sent for EC after a positive CTC exam. The mean number of monthly colonoscopies with polypectomy remained constant after the introduction of CTC (197.0 vs 180.2). Monthly referrals for screening EC exams initially decreased but were unchanged 3 yr after institution of a CTC screening program (255.0 vs 253.5). CONCLUSIONS: (a) In our tertiary care center the initiation of a screening CTC program did not result in a decrease in the number of total colonoscopy exams, screening colonoscopy exams performed, nor requests for screening colonoscopy. (b) Only a small number of CTC exams were referred for EC with polypectomy, therefore a CTC screening program may not increase the overall number of therapeutic colonoscopies performed.