Patients with gastroesophageal reflux disease (GERD) receive long-term therapy with proton pump inhibitor (PPI) agents. Several studies have recently been published suggesting that treatment with PPI may cause bone fractures, although the number of prospective studies in this regard is limited. The aim of this study is to prospectively investigate the effect of PPIs on bone density. Between March 2009 and January 2011, 114 GERD patients (18-56 years) and 110 healthy controls were included in the present study. Bone mineral densitometry (BMD) by using dual-energy X-ray absorptiometry was assessed at lumbar spine and femur neck. BMD measurements were performed on all subjects at the beginning of the study. The patients were divided according to three drugs by their treatment with esomeprazole, lansoprazole, or pantoprazole. The study group was followed for at least 6 months on PPI therapy, and then BMD measurements were repeated. The mean duration of treatment with PPIs was 8.5 +/- A 2.3 months. In patients receiving PPIs, the mean reduction in total vertebra T score following treatment compared to pre-treatment values was 00.23 +/- A 0.42 units (95 % CI 0.15-0.30) (p < 0.01), while the mean reduction in the femur T score was 0.10 +/- A 0.40 units (95 % CI 0.03-0.18) (p = 0.03). Reduction following treatment in L4 and total vertebra T scores of lansoprazole group was significantly higher than of pantoprazole group (p = 0.04). Reduction in femur T score of esomeprazole group was higher than of lansoprazole group and pantroprazole group, but it is not statistically significant. Treatment with a PPI results in a significant reduction in bone density. Close monitoring is beneficial for patients who are to receive long-term treatment with PPI.