The objective of this study was to compare the changes on bone mineral density, and the effects on persistence and adverse events in patients treated for postmenopausal osteoporosis with generic alendronate or with branded alendronate (Fosamax®) or branded risedronate (Actonel®) once weekly. In this retrospective patient chart analysis, we reviewed the 1-year observational treatment results for 186 women (ITT population) with postmenopausal osteoporosis. Patients from our outpatient department, who had started with once-weekly bisphosphonate therapy between 36 and at least 12 months before this chart review, were included in this comparative three-arm study according to their treatment: A, Generic Alendonate 70 mg products; B, Branded Alendronate (Fosamax®) 70 mg once weekly and C, Branded Risedronate (Actonel®) 35 mg once weekly. All patients received basic therapy with 1,200 mg calcium and 800 IU vitamin D per day. Patient’s bone mineral density (BMD) at lumbar spine and total hip was below −2.5 T-score, and they were with or without prevalent vertebral and non-vertebral fractures. Data analysis regarding the 186 patients shows an average increase in LS-BMD after 12 months of 2.8, 5.2 and 4.8% for the groups A, B and C, respectively. The respective mean changes at total hip were 1.5, 2.9, and 3.1%. At both sites, the mean increases in BMD were not different between the two groups receiving branded bisphosphonates (B, C) but for both were significantly higher than for the group treated with generic alendronate (A). At 12 months, 68% of group A, 84% of group B and 94% of group C were still on bisphosphonate therapy. The persistence of patients treated with generic alendronate was significantly lower as compared to each of the two with branded bisphosphonate-treated groups. The total numbers of patients reporting gastrointestinal adverse events were 32, 15 and 9 for group A, group B, and group C, respectively. Significantly lower increases of lumbar spine and total hip BMD with generic alendronate once weekly as compared to the two branded bisphosphonate originals (Fosamax®, Actonel®) were observed. The reasons for the 40–50% lower BMD increase rates when using the generic compounds are not known yet. At least in part the lower efficacy can be explained by a significantly lower degree of persistence with generic alendronate, which could be related to a higher incidence of gastrointestinal adverse events. Other reasons could be lower bioavailability or potency of generic alendronate.