Background The frequency of upper gastrointestinal (GI) tract involvement in Crohn`s disease (CD) has been reported with a large variation. Risk factors and disease course of patients with upper GI tract involvement remain largely elusive. Methods Data on CD patients in the Swiss Inflammatory Bowel Disease Cohort were analyzed. Patients with upper GI tract involvement were compared to controls. Logistic regression models for prediction of upper GI tract involvement and Cox proportional hazard models for occurrence of complications were computed. Results We included 1638 CD patients, of whom 107 (6.5%) presented with upper GI tract involvement at the time of diagnosis and 214 (13.1%) at any time. Prevalence of such involvement at diagnosis increased over time (5.1% for 1955-1995 vs. 11.3% for 2009-2016). In a multivariate logistic regression model, male sex and diagnosis between 2009-2016 (vs. before 1995) were independent predictors for presence of upper GI tract involvement at CD diagnosis (OR 1.600, p=0.021 and OR 2.686, p<0.001), while adult age was a negative predictor (OR 0.388, p=0.001). Patients with upper GI tract involvement showed a disease course similar to control patients (HR for any complications 0.887 [95% CI 0.409-1.920]), and a trend towards occurrence of fewer intestinal fistulas (log-rank test p=0.054). Conclusions Prevalence of upper GI tract involvement has been increasing over the past decades. Male sex and young age at diagnosis were identified as the main predictive factors for such involvement at CD diagnosis. Involvement of upper GI tract did not result in a worse outcome.