Large-scale chemoprevention of peptic ulcer disease and gastric cancer through eradication of Helicobacter pylori would expose large population groups to antibiotics, which raises concerns about possible dissemination of antibiotic resistance. The objective of this cohort study was to determine whether a triple therapy, containing omeprazole, clarithromycin, and metronidazole, of H. pylori infection increases the prevalence of macrolide resistance in the normal microbiota. 85 patients with a peptic ulcer disease with verified H. pylori infection and 12 dyspeptic patients without positive findings upon endoscopy were included. Minimal inhibitory concentrations of clarithromycin for Staphylococcus, Streptococcus, Enterococcus and Bacteroides spp. were determined from samples taken before and after treatment, and 1 y later. Before treatment, macrolide resistance was observed in 11%, 31%, 9% and 11% of the staphylococci, streptococci, enterococci and Bacteroides, respectively. The number of resistant isolates remained elevated after 1 y, most notably for staphylococci and streptococci. No development of persistent resistance was detected in the untreated control group. Triple therapy including clarithromycin leads to persistent macrolide resistance in the normal microbiota. A prevalent pool of resistance genes in the normal microbiota constitutes an ecological hazard that needs to be considered before global treatment programmes for eradication of H. pylori are implemented.