BACKGROUND: Proton-pump inhibitor (PPI) use for management of gastroesophageal reflux disease (GERD) consists of a short-duration trial, according to guidelines. Long-term usage is appropriate under certain indications. Literature has increasingly documented an adverse effect profile of PPIs, including kidney disease and bone fragility. OBJECTIVE: To investigate the rate of occurrence of osteopenia, osteoporosis, and chronic kidney disease (CKD) in patients using PPI therapy for longer than the recommended trial period of 8 weeks. METHODS: Retrospective cohort analysis of a single-site primary care clinic. Patients aged 18 to 65 years with PPI prescriptions longer than 8 weeks were included. Information regarding PPI prescriptions, demographics, and medical diagnoses was collected. RESULTS: The search discovered 293 PPI-users and 1908 never-PPI-users. Demographics varied, with a CONCLUSIONS AND RELEVANCE: We observed increased occurrence rates of osteoporosis, or osteopenia, and CKD in patients with prolonged PPI use. Demographics varied in age, BMI, and black race proportion. A logistic regression revealed increased likelihood of kidney disease and osteoporosis/osteopenia in association with PPI use. These results add to the evidence regarding long-term PPI use and the development of these conditions, but additional studies are needed.