BACKGROUND & AIMS: Cancelled and missed colonoscopy appointments waste resources, increase colonoscopy delays, and can adversely affect patient outcomes. We examined individual and organizational factors associated with missed and cancelled colonoscopy appointments in Veteran Health Administration facilities. METHODS: From 69 facilities meeting inclusion criteria, we identified 27,994 patients with colonoscopy appointments scheduled for follow-up, on the basis of positive fecal occult blood test results, between August 16, 2009 and September 30, 2011. We identified factors associated with colonoscopy appointment status (completed, cancelled, or missed) by using hierarchical multinomial regression. Individual factors examined included age, race, sex, marital status, residence, drive time to nearest specialty care facility, limited life expectancy, comorbidities, colonoscopy in the past decade, referring facility type, referral month, and appointment lead time. Organizational factors included facility region, complexity, appointment reminders, scheduling, and prep education practices. RESULTS: Missed appointments were associated with limited life expectancy (odds ratio [OR], 2.74; P = .0004), no personal history of polyps (OR, 2.74; P < .0001), high facility complexity (OR, 2.69; P = .007), dual diagnosis of psychiatric disorders and substance abuse (OR, 1.82; P < .0001), and opt-out scheduling (OR, 1.57; P = .02). Cancelled appointments were associated with age (OR, 1.61; P = .0005 for 85 years or older and OR, 1.44; P < .0001 for 65-84 years old), no history of polyps (OR, 1.51; P < .0001), and opt-out scheduling (OR, 1.26; P = .04). Additional predictors of both outcomes included race, marital status, and lead time. CONCLUSIONS: Several factors within Veterans Health Administration clinic control can be targeted to reduce missed and cancelled colonoscopy appointments. Specifically, developing systems to minimize referrals for patients with limited life expectancy could reduce missed appointments, and use of opt-in scheduling and reductions in appointment lead time could improve both outcomes.