An association between hematological cancers and inflammatory bowel disease (IBD) has previously been suggested, but the risk of IBD in patients with myeloproliferative neoplasms (MPNs) is unknown. We conducted a nationwide population-based cohort study using Danish registries, to estimate the risk of IBD in individuals diagnosed with essential thrombocythemia, polycythemia vera, myelofibrosis or unclassifiable MPN during 1994-2013. MPN patients were matched 1:10 with sex- and age-matched comparisons. Everyone was followed until a diagnosis of IBD, death/emigration, or 31 December 2013. The risk of IBD overall and according to MPN subtype was calculated using Cox regression and presented as hazard ratios (HRs) with 95% confidence intervals (CI). Of 8207 MPN patients followed for 45,232 person-years, 80 were diagnosed with IBD (61 ulcerative colitis, 19 Crohn's disease). The rate of IBD per 1000 person-years was 1.8 (95% CI:1.4-2.2) in patients vs. 0.8 (95% CI:0.7-0.8) in comparisons, and the absolute 10-year risk of IBD was 0.8% (95% CI:0.6-1.0) in patients vs. 0.4% (95% CI:0.4-0.5) in comparisons. The HR of IBD was 2.4 (95% CI:2.1-2.9) with similar HRs for ulcerative colitis and Crohn's disease. MPN subtype risks varied from 2.1 (95% CI:1.6-2.7) to 2.8 (95% CI:2.1-3.7). Our unselected cohort study showed a more than 2-fold increased risk of IBD in MPN patients.