As long as you aren't in your first trimester of pregnancy at the time of the vaccination, you should be fine. I would go in for a blood serum test and use protection while waiting for the results just to make sure before getting the shot.
I am 6.5 wks and I had a dr. appt. last Friday and asked my dr. the SAME EXACT question. He said that yes you could get a shot, but it's not worth it this time because they "missed the boat" on this year's flu vacc. I do think that he did not go into details about that there are some possible risks to having the shot early on in pregnancy, but what I got out of it is that IF the vaccine was more accurate, then he would of suggested getting the vaccine. Apparently as long as it is a "dead" virus, it is okay. I work p/t at vet's office and I was worried about accidentally poking myself with a rabies vacc. and he said even that would not cause any harm because it is a dead virus. So I would think it's safe to get the flu vacc. if you really feel like you need it.
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