Background and Aims The associations between gastrointestinal diseases (GIs) and cardiovascular disease (CVD) were unclear. We conducted a prospective cohort study to explore their associations. Methods This study included 340,862 individuals without baseline CVD from the UK Biobank cohort. Individuals with and without GIs were followed up until the ascertainment of incident CVDs, including coronary heart disease (CHD), cerebrovascular disease (CeVD), and peripheral artery disease (PAD). The diagnosis of diseases was confirmed with combination of the nationwide inpatient data, primary care data, and cancer registries. A multivariable Cox proportional hazard regression model was used to estimate the associations between GIs and the risk of incident CVD. Results During a median follow-up of 12.4 years, 28,787 incident CVD cases were diagnosed. Individuals with GIs had an elevated risk of CVD (hazard ratio 1.38; 95% confidence interval 1.35-1.42, P<0.001). Eleven out of fifteen GIs were associated with an increased risk of CVD after Bonferroni-correction, including cirrhosis, non-alcoholic fatty liver disease, gastritis and duodenitis, irritable bowel syndrome, gastroesophageal reflux disease, peptic ulcer, celiac disease, pancreatitis, diverticular disease, biliary disease, and appendicitis. The associations were stronger among women, individuals aged ≤ 60 years, and those with body mass index ≥ 25 kg/m2. Conclusions This large-scale prospective cohort study revealed the associations of GIs with an increased risk of incident CVD, in particular CHD and PAD. These findings support the reinforced secondary CVD prevention among patients with gastrointestinal disorders.