Background: Globally, the incidence rates of inflammatory bowel disease (IBD) are increasing; however, data from high-incidence areas are conflicting. Previous studies in Denmark have assessed incidence rates of Crohn's disease (CD) and ulcerative colitis (UC) using short observation periods. Aim: To investigate trends in IBD incidence in Denmark over a thirty-year period using nationwide data. Methods: Patients diagnosed with CD or UC in Denmark between 1980 and 2013 were identified in the Danish National Patient Registry (NPR) and included in a nationwide cohort. Incidence rates estimated using different numbers of National Patient Registry records (≥1, 2, 3 or 4) required for case definition were compared. Results: From 1980 to 2013 the incidence of CD increased from 5.2 (95% CI: 5.0–5.4) per 100 000 to 9.1 (95% CI: 8.7–9.5) per 100 000 and the incidence of UC increased from 10.7 (95% CI: 10.4–11.0) per 100 000 to 18.6 (95% CI: 18.0–19.2) per 100 000. The increased incidence in CD and UC was independent of gender. The annual increase in incidence rate was greatest in patients aged <15 years for CD and those older than 15 years for UC. For both CD and UC the incidence rates for females were significantly higher than for males. The number of registry records chosen to define IBD cases greatly influenced incidence estimates. Conclusions: The incidence of IBD in Denmark continues to increase and is among the highest in the world. Using at ≥2 records of IBD diagnosis in the Danish National Patient Registry will result in more valid incidence estimates.