Objective: The occurrence of Helicobacter pylori (HP) and clarithromycin resistant HP (crHP) have not been investigated longitudinally in the Swedish childhood population. The aims were to study the prevalence of gastric HP-DNA and crHP strains in a cohort of children living in the southernmost parts of Sweden who were investigated with upper endoscopy between 2005 and 2016. Methods: HP colonisation and crHP in 1768 children who underwent 1887 endoscopic procedures with gastric biopsies, of whom 393 were referred for abdominal pain, gastritis, ulcer or gastrointestinal bleeding (Group I) and 1494 were referred for other reasons (Group II). The occurrence of HP-DNA from gastric biopsies was given as a global prevalence as information on previous eradication were missing. Results: The global prevalence of HP-DNA was 222/1887 (11.8%; 95% CI 10.4%-13.3%) of which 46/ 222 (20.7%; 95% CI 15.9%-26.5%) were crHP. The prevalence of HP-DNA in Group I was 141/393 (35.9%; 95% CI 31.3%-40.7%), which was higher compared with that of 81/1494 (5.4%; 95% CI 4.4%-6.7%) in Group II (p < .0001). crHP strains occurred equally frequent in the biopsies in both groups and found in 29/141 (20.6%; 95% CI 14.7%-28.0%) in Group I and 17/81 (21.0%; 95% CI 13.5%-31.1%) in Group II, respectively (p > .9999).Conclusions: More than one in every ten (12%) children investigated with upper endoscopy in the southernmost parts of Sweden were gastric HP-DNA positive of which 21% were crHP regardless of indication for investigation. Clarithromycin is therefore not recommended as first line empirical treatment for eradicating an HP infection in children. ARTICLE HISTORY