The pathogenesis of primary sclerosing cholangitis (PSC), a severe autoimmune liver disease, remains largely unknown. Infection with Helicobacter pylori (H. pylori) and subsequent gastritis could act as a triggering event of PSC, as H. pylori seems to be more prevalent in chronic liver disease. However, the risk of PSC among patients with gastritis and its precursor, H. pylori infection, is undetermined. In this nationwide cohort study, we included Swedish individuals undergoing a gastroscopy with biopsy during 1990-2017 showing gastritis (n = 306 588) or H. pylori (n = 11 890). Three control groups were used (1) matched controls from the Swedish general population (n = 1 544 667), (2) individuals with a gastric biopsy indicating normal mucosa (n = 318 754) and (3) sibling controls (n = 231 879). We calculated the hazard ratios (HRs) for PSC development, adjusting for age, sex, calendar year, county, comorbidities, alcohol-related disorders, education, and country of birth. Patients with a histological diagnosis of gastritis or H. pylori were more likely to be diagnosed with PSC during follow up. Compared to the general Swedish population, the fully adjusted HR for PSC among patients with gastritis was 3.35 (95% CI 2.67-4.20). However, compared to secondary controls with a normal gastric mucosa, the PSC risk was not increased among patients with gastritis. Patients with a gastroscopy biopsy showing gastritis have a moderately increased risk for PSC later in life but not compared to other individuals undergoing gastrointestinal work up ("normal mucosa)". The association with PSC may be non-specific and apply to several gastrointestinal disorders.