Is it safe to take alendronate if I have a history of acid reflux? I know not to lay down for 1/2 hour.

Yes. Alendronate can cause irritation of the esophagus and stomach and cause erosions. You can take the medications but must monitor closely for symptoms such as burning of throat or stomach or dark stools. You may also consider being on antacid medication to protect your stomach. speak with your PCP regarding other classes of medications. Make sure you have good calcium, vit d levels and exercise.