I had taken 1 cycle of clomid while I was already unknowingly pregnant. Can you tell me what the side effects or consequences would be to my baby? I took the clomid while I was 3 weeks pregnant and I had a full period so I took the clomid from day 4 to day 8 of my menstral period. I later found out that I was 3 weeks further along than I thought, and therefore realized that I was already pregnant when I took clomid.