Background The use of proton pump inhibitors (PPIs) is extensive. While the incidence of new treatments remains stable, the prevalence of long-term treatment is rising. Studies have shown that up to 70% of patients on chronic acid suppression lack a verified indication for treatment. Aims To investigate primary care patient characteristics associated with long-term use of PPIs. Methods A cross-sectional analysis of 42 634 patients registered with 22 general practitioners was performed. Patients with prescriptions of ≥120 tablets/year were defined as long-term users. A survey of a subgroup of patients without verified indication was performed. Results In all, 901 (2.1%) patients were long-term treated. Verified indications for treatment were identified for 247/901 (27%). An upper GI endoscopy had been performed in 418 patients (46%). Of the 194/654 without verified indication who participated in the survey, 71% reported heartburn/acid regurgitation as the reason for therapy. On-demand therapy was reported by 43/194 (22%) and previous attempts to withdraw by 119/194 (61%). Conclusions The prevalence of PPI long-term treatment among primary care patients is 2.1%. The main reason for treatment is reflux symptoms or verified GERD. Rationalization of use of PPIs is possible as daily treatment without attempts to discontinue is frequently observed.