Summary Chronic obstructive pulmonary disease (COPD) and systemic glucocorticoid exposure are well-known risk factors of osteoporosis. We evaluated alendronate prescription practices related to COPD and exposure to systemic corticosteroids from 1996 to 2008 and showed an increasing targeting of alendronate treatment in patients with COPD and patients with systemic corticosteroid exposure. Introduction COPD and systemic glucocorticoid exposure are well-known risk factors of osteoporosis and fragility fracture, but osteoporosis is often underdiagnosed and undertreated in these patients. This study aims to evaluate alendronate prescription practices related to COPD and/or to exposure to systemic glucocorticoids among Danish women. Methods A total of 388,314 female subjects >50 years old, 64,719 of whom initiated treatment with alendronate, and 323,595 age- and gender-matched controls were retrospectively identified between 1996 and 2008 from national health registers. Multivariate logistic regression was used for examining prescription practices, specifically if these risk factors (COPD or glucocorticoid exposure) increased or decreased the likelihood of beginning alendronate therapy. Results A diagnosis of COPD was associated with an increased likelihood of using alendronate (odds ratio (OR) 1.4, 95 % confidence interval (CI) 1.4–1.5, p < 0.001). Further, a diagnosis of COPD was associated with an increasing tendency of initiating alendronate treatment in the study period (OR 1.3 (95 % CI 1.1–1.5, years 1996–1999) to 1.5 (95 % CI 1.4–1.6, years 2006–2008), p < 0.01). Exposure to systemic glucocorticoids was associated with a significantly increasing (OR 3.6, 95 % CI 3.3–3.9 to OR 5.5, 95 % CI 5.3–5.8) probability of receiving alendronate treatment in the same observation period. Conclusion This nationwide register-based study on alendronate prescription practices in Denmark shows an increasing targeting of alendronate treatment in patients with COPD and an even stronger trend for patients with systemic glucocorticoid exposure, perhaps indicating increased awareness of well-known and associated conditions.