Coexistence of inflammatory bowel disease (IBD) in atopic dermatitis (AD) patients has been reported. The long-term risk of IBD in AD patients remains unclear. Our aim for the study is to examine the long-term risk of IBD in AD patients. This is a nationwide cohort study. From the National Health Insurance Research Database of Taiwan (1997–2013), a total of 36 400 AD patients were identified and matched with 364 000 reference subjects without AD by age, sex and number of hospital visits. Demographic characteristics and comorbidities were compared. Cox proportional hazards regression analysis was conducted to examine the risk of IBD. The 16-year cumulative incidences of IBD were 0.047% (95% confidence interval [CI], 0.040–0.054) and 0.047% (95% CI, 0.025–0.096) in non-AD and AD cohorts, respectively (P = 0.973). There were 17 cases of IBD (0.05%), including 10 ulcerative colitis and seven Crohn’s disease, among AD patients compared with 169 IBD cases (0.05%) among controls (P > 0.999). Infections (adjusted hazard ratio [HR], 2.71; 95% CI, 1.96–3.95; P < 0.001) and age (adjusted HR, 1.03; 95% CI, 1.02–1.03; P < 0.001) were independently associated with IBD, after adjusting for major comorbidities and conducting multivariate analyses. AD was not associated with IBD development. In conclusion, AD is not independently associated with IBD development.