OBJECTIVE: To examine alendronates side-effect profile and effect on bone mineral density (BMD) in deflazacort-treated boys with Duchennes muscular dystrophy (DMD) and low BMD. DESIGN: Before-after trial. SETTING: Neuromuscular clinic at a children’s hospital in Canada between 1999 and 2000. PARTICIPANTS: All consenting boys with DMD who had z scores less than -1.00 (spine and/or total body) and in whom BMD testing was feasible. INTERVENTION: Boys received .08 mg.kg(-1) .d(-1) of alendronate orally, with 750 mg of daily calcium and 1000 IU of vitamin D. BMD, height, weight, physical activity, Tanner stage, and adverse effects were followed for 2 years. MAIN OUTCOME MEASURES: BMD z scores at the lumbar spine (L1-4) and total body. RESULTS: Of the 42 eligible boys assessed, 23 had low BMD; for 16 of the 23, future BMD testing was feasible. Mean age was 10.8 years (range, 6.9-15.6 y). Mean baseline z scores at the total body and spine were -0.80 and -1.94, respectively. At 2 years, mean z scores were unchanged. Furthermore, alendronate response varied by baseline age. In multivariable analysis, improvement in total body and spine z scores was associated with younger age at baseline ( P =.01 for both). CONCLUSIONS: In deflazacort-treated boys, alendronate had a positive effect on BMD z scores; the effect was greatest when given early in the course of disease.