The U.S. Multi-Society Task Force on Colorectal Cancer sets a target of cecal intubation in at least 90% of colonoscopies. We conducted a population-based study to determine the colonoscopy completion rate and to identify factors associated with incomplete procedures. Men and women 50 to 74 years of age who underwent a colonoscopy in Ontario between January 1, 1999, and December 31, 2003, were identified. The first (index) colonoscopy was classified as complete or incomplete. A generalized estimating equations model was used to evaluate the association between patient, endoscopist (specialty, colonoscopy volume), and setting (academic hospital, community hospital, private office) factors and incomplete colonoscopy. A total of 331,608 individuals had an index colonoscopy, of which 43,483 (13.1%) were incomplete. Patients with an incomplete colonoscopy were older (odds ratio [OR] 1.20 per 10-year increment; 95% confidence interval [CI]=1.18-1.22), more likely to be female (OR 1.35; 95% CI: 1.30-1.39), have a history of prior abdominal surgery (OR 1.07; 95% CI: 1.05-1.09) or prior pelvic surgery (OR 1.04; 95% CI: 1.01-1.06). For colonoscopies done in a private office, the odds of an incomplete procedure were more than 3-fold greater than for procedures done in an academic hospital (OR 3.57; 95% CI: 2.55-4.98). In usual clinical practice in Ontario, 13.1% of colonoscopies are incomplete. The factors most strongly associated with incomplete colonoscopy were increased patient age, female sex, and having the procedure in a private office. Quality improvement programs are needed to improve colonoscopy completion rates.