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Population-based studies of site-specific cancer risk in patients with inflammatory bowel disease (IBD) according to IBD phenotype and treatment are lacking. We studied cancer risk in a well-characterized population-based IBD cohort from North Jutland County, Denmark.A total of 1,515 patients were diagnosed with ulcerative colitis (UC) and 810 with Crohn’s disease (CD) during 1978–2002. Patients were followed until 31 December 2010 for occurrence of incident cancer, identified in the Danish Cancer Registry. Observed numbers of cancer were compared with expected numbers (based on age- and sex-specific background rates) and presented as standardized incidence ratios (SIRs) with 95% confidence intervals (CIs).Patients with UC were not at increased risk of cancer overall (SIR, 1.12; 95% CI, 0.97–1.28) despite increased risk of prostate cancer (SIR, 1.82; 95% CI, 1.17–2.71). Patients with CD had a 55% increased risk of cancer overall (SIR, 1.55; 95% CI, 1.29–1.84) related to young age, colonic disease, smoking, and thiopurine exposure. Patients were at increased risk of small bowel cancer (SIR, 15.18; 95% CI, 1.84–54.78), lung cancer (SIR, 2.13; 95% CI, 1.19–3.52 (associated with female gender and smoking)), colorectal cancer in males (SIR, 2.43; 95% CI, 1.05–4.78), cervical dysplasia (SIR, 1.65; 95% CI, 1.10–2.37 (associated with young age at diagnosis, smoking, 5-aminosalicylic acid, and thiopurine exposure)), and non-Hodgkin lymphoma (SIR, 3.43; 95% CI, 1.38–7.07 (unrelated to thiopurine exposure)).Patients with CD, but not UC, have an overall excess risk of cancer. Clinical characteristics of IBD patients at excess risk differ by cancer subtype.