Proton pump inhibitors (PPIs) are the most effective drugs for treating acid-related diseases. In recent decades, the use of PPIs has increased exponentially. For a long time, PPIs were considered completely safe drugs for both short-term and long-term use. However, modern clinical guidelines note that when prescribing PPIs in large doses for a long period, the possibility of side effects should be taken into account. In recent years, a number of foreign reviews have been published that examine the associations between PPIs and a number of diseases/conditions. We searched the PubMed and Scopus information databases for publications on the safety of PPI use, including sources up to January 30, 2024. In this review, we examined the effect of long-term use of PPIs on the urinary system. This review demonstrates possible changes in the urinary system and an increased risk of developing nephrolithiasis, acute interstitial nephritis, acute kidney injury, chronic kidney disease, end-stage renal failure with long-term use of PPIs, which should certainly be taken into account when prescribing them for a long period, especially in patients with comorbid pathology.