Doxycycline Hyclate Side Effects: I started taking doxy for my acne but developed severe headaches http://www.medications.com/effect/view/39941 I started taking doxy for my acne but developed severe headaches about a week into treatment. At first, I thought it was because I was pretty stressed with college and not sleeping much but I noticed I would get a headache at about the same time after takin How are you doing now? and what are you taking to get better? I t Mon, 23 Mar 2009 09:17:32 -0400 http://www.medications.com/effect/view/39941?item=18349 How are you doing now? and what are you taking to get better? I to have bad side affects. Sorry you are going through this it is bad. http://www.medications.com/effect/view/39941?item=18349