My son takes Doxycycline twice a day for severe acne. It will make him throw up too. He has to take it with milk and he also takes Ranitidine (generic Zantac) 2 times a day. You may want to talk to your doc about getting something for your stomach. I don't care what you take your meds with they will often still tear up your stomach, some it doesn't bother but Doxy. is strong stuff. I take Prilosec OTC (with scrip) once a day and it is the only thing that helps. If you don't like taking meds with milk (I don't) then you can try taking your stomach med (I know, not another med) maybe a half an hour before you take anything else. It is worth a try. Good luck.