ObjectiveThe objective of this study was to analyze the comparative gastrointestinal tolerability of proprietary versus generic alendronate in patients treated for primary osteoporosis. MethodsThe study was based on all patients starting therapy with alendronate in Sweden between 2005 and 2009. The primary outcome measure was the start of treatment with a gastroprotective agent and the secondary outcome was hospitalization for gastrointestinal adverse event (GIAE). The incidence of both outcomes was measured within the first six months after the initiation of the alendronate treatment. ResultsThe crude incidence of gastroprotective treatment during the first six months following the start of the alendronate therapy was 5.45% (bootstrapped CI95 4.09%–7.19%) and 5.04% (bootstrapped CI95 4.74%–5.38%) for patients prescribed proprietary and generic alendronate, respectively. The crude six-month incidence of hospitalization for GIAE was 0.43% (bootstrapped CI95 0.14%–1.29%) and 0.71% (bootstrapped CI95 0.55%–0.91%) for proprietary and generic alendronate, respectively. Controlling for age, sex, and other available covariates, there was no significant difference in the risk of GIAEs between proprietary and generic alendronate. ConclusionsNo significant difference in the incidence of GIAEs was identified between patients prescribed proprietary and generic alendronate between 2005 and 2009 in Sweden. More research is needed to provide conclusive evidence of the gastrointestinal tolerability profiles of proprietary and generic alendronate.