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i would definitely speak to your doc before continuing with it, but before you freak out let me tell you i was just on doxycycline during my ivf cycle - i took it from after retrieval and just took my last one yesterday morning (right before transfer). I would think if they were so worried about it so early in pregnancy they'd be cautious to prescribe in an ivf cycle, but then again i did finish it right before the transfer, but probably still had some of it in system by transfer and after. so just ask your dr. so you can ease your mind. i'm sure you're ok now. maybe he'll just tell you not to continue. speak to him.
Heres the website on safefetus.com
http://www.safefetus.com/DrugDetail.asp?DrugId=330&TradeName=Doxycin&TradeId=3838
Doxycycline is a category D so consult your Dr right away.