Should my girlfriend wait until after her gardasil shot to have sex?

It would be safer: Gardasil is a 3-shot vaccine that prevents infection from 2 strains of HPV virus that cause cervical cancer, and 2 strains that cause genital warts. It also prevents anal warts (and maybe anal cancer) due to the same strains, in both men and women. The antibodies one produces from the vaccine flow in the bloodstream everywhere. Other body sites are probably protected, but this has not been proven.

Yes: Yes, it is best to wait until fully protected.