Nausea and vomiting are common side effects of doxycycline. If you vomit after taking doxycycline, you should carry on with the prescribed course. Although doxycycline can make you sick, partial absorption or missing one dose is unlikely to have an effect on the success of treatment. Try taking doxycycline after a meal to reduce feelings of nausea. If you throw up more than once, you should contact your doctor as you may need to try a different treatment.