Background: Low adherence to bisphosphonate therapy is associated with increased fracture risk. Factors associated with discontinuation of osteoporosis medications have not been studied in-depth. This study assessed medication discontinuation and switching patterns among Medicare beneficiaries who were new users of bisphosphonates and evaluated factors possibly associated with discontinuation. Methods. We identified patients initiating bisphosphonate treatment using a 5% random sample of Medicare beneficiaries with at least 24 months of traditional fee-for-service and part D drug coverage from 2006 through 2009. We classified medication status at the end of follow-up as: continued original bisphosphonate, discontinued without switching or restarting, restarted the same drug after a treatment gap (≥ 90 days), or switched to another anti-osteoporosis medication. We conducted logistic regression analyses to identify baseline characteristics associated with discontinuation and a case-crossover analysis to identify factors that precipitate discontinuation. Results: Of 21,452 new users followed respectively for 12 months, 44% continued their original therapy, 36% discontinued without switching or restarting, 8% restarted the same drug after a gap greater than 90 days, and 11% switched to another anti-osteoporosis medication. Factors assessed during the 12-month period before initiation were weakly associated with discontinuation. Several Factors measured during follow-up were associated with discontinuation, including more physician visits, hospitalization, having a dual-energy X-ray absorptiometry test, higher Charlson comorbidity index scores, higher out-of-pocket drug payments, and upper gastrointestinal problems. Patterns were similar for 4,738 new users followed for 30 months. Conclusions: Among new bisphosphonates users, switching within and across drug classes and extended treatment gaps are common. Robust definitions and time-varying considerations should be considered to characterize medication discontinuation more accurately. © 2014 Yun et al.; licensee BioMed Central Ltd.