I took two pills for chlamydia at 6 pm, known as azithromycin, and flagyll at 8:30 pm, i threw up at 11:40 pm. are they still in my system?

Probably OK: No problem for azithromycin and chlamydia; enough is absorbed even within 30-60 minutes. Metronidazole (Flagyl) does not treat chlamydia. If you were prescribed a single dose of 2 g, your doctor must have also diagnosed or suspected trichomonas, and probably enough drug was absorbed. Check back with your doctor if Flagyl was prescribed 2-3 times a day (PID? BV?).

Probably the : first two pills, yes, the second pill maybe not. If unsure get retreated, and consider eating prior to taking pills.