Observational studies have reported associations between atopic diseases, including allergic rhinitis (AR), asthma, atopic dermatitis (AD), and inflammatory bowel disease (IBD), but the causal relationship remains unknown. We utilized pooled data from genome-wide association studies, qualified instrumental variables were screened according to the 3 hypotheses of MR, and bidirectional causality between atopic diseases and IBD was assessed using 2-sample Mendelian randomization analysis (2SMR). The results of our study suggest that AR increased the risk of Crohn disease (CD) (IVW OR = 1.19, 95% CI = 1.02–1.39, P = .026), ulcerative colitis (UC) (IVW OR = 1.14, 95% CI = 1.01–1.29, P = .031) and overall IBD (IVW OR = 1.15, 95% CI = 1.03–1.28, P = .015); Asthma increased the risk of CD (IVW OR = 7.66, 95% CI = 1.58–37.20, P = .012), UC (IVW OR = 3.81, 95% CI = 1.09–13.32, P = .036) and overall IBD (IVW OR = 5.13, 95% CI = 1.48–17.70, P = .010); AD increased the risk of CD (IVW OR = 1.19, 95% CI = 1.02–1.39, P = .023) and overall IBD (IVW OR = 1.14, 95% CI = 1.03–1.28, P = .015) risk. In reverse causality, only CD increased the risk of AR (IVW OR = 1.02, 95% CI = 1.00–1.05, P = .031). This study shows that atopic diseases of AR and asthma are causally related to IBD and its subtypes, and AD is causally related to IBD (which may be attributed to CD). Of the reverse causality, only CD was causally related to AR.