Welcome to the STD forum. Sorry to hear your difficulties and uncertainties about your genital warts. Try not to let it get you down; this won't go on indefinitely and all will be well. And congratulations on starting Gardasil.
Warts are not especially common in the vagina, except on the cervix. If visible warts haven't appeared in those locations by now, most likely they will not. Any additional warts that you develop will not be from re-catching the virus from your partner. All HPV infections are more widespread than meets the eye -- if new lesions do appear, it will be because you are already infected at those spots.
Not being able to use Aldara doesn't much matter; don't worry about it. No treatment, including imiquimod (Aldara), is more than about 60-70% effective. In theory, Aldara might be better at preventing recurrent warts, but in the real world there is no obvious difference in cure rate or recurrence rate between Aldara and any other treatment. If one method isn't working well, trying another makes sense. Aside from podophyllin and Aldara, other options are freezing, repeated laser- or electrocautery, and trichloroacetic acid.
1) Any warts that continue to appear probably will be from the infection you already have, not re-catching the virus from your partner.
2) You can use Aldara anywhere in the genital area. Aldara causes more inflammation as a side effect than some other treatments, in which case there might be some uncomfortable urination. But no serious side effects are likely.
3) I can't get into such specific treatment recommendations. Each case and each patient are different. This is something to discuss with the doctor who is treating you with podophyllin and prescribing Aldara. (In general, I avoid using more than one treatment at a time.)
4) Genital warts, and the underlying HPV infection, generally stop recurring within a few months and pretty much always clear up within a year or so.
Dermatologists generally have the greatest experience with persistent or recurrent warts and the broadest range of experience with multiple treatment options. If new warts continue to appear and/or existing ones aren't clearing up promptly, consider asking for referral to a dermatologist.
I hope this helps. Best wishes-- HHH, MD
Dear Dr. Handsfield,
Thank you for your quick response. Your answers are thorough and complete. Thank you very much.
Thanks for the thanks. I'm glad to have helped. Take care.