Remember that I am not your regular physician. I do not have all the clinically relevant information. The below is simply my opinion on the limited information that you have provided me.

Gardasil is classified as a “pregnancy category” B2 substance which means that it is a medication “… that have been taken by only a limited number of pregnant women and women of childbearing age, without an increase in the frequency of malformation or other direct or indirect harmful effects on the human fetus having been observed. Studies in animals are inadequate or may be lacking, but available data show no evidence of an increased occurrence of fetal damage.”

In the existing trials of Gardasil, women who fell pregnant during the vaccination course did not appear to have experienced an increased rate of foetal abnormality or miscarriage. However, those trials were not looking for this specifically. I believe that the recommendation in this setting is to delay the further two doses of Gardasil until after delivery.

From MIMS prescribing information (1):

Female rats were given the clinical dose of Gardasil (500 microL) intramuscularly twice (during early gestation and one week postnatal) or four times (five and two weeks prior to mating, during early gestation and one week postnatal). Maternal toxicity or adverse effects on offspring were not observed. High titers of HPV type specific antibodies were detected in maternal blood during gestation, in near term fetal blood and in blood of offspring at weaning and at eleven weeks postnatal, indicative of transplacental and lactational transfer of antibodies (see Use in lactation). The effect of Gardasil administration of vaccine treated males on offspring has not been studied.

In clinical studies, women underwent urine pregnancy testing prior to administration of each dose of Gardasil. Women who were found to be pregnant before completion of a three dose regimen of Gardasil were instructed to defer completion of their vaccination regimen until resolution of the pregnancy. Such nonstandard regimens resulted in postdose 3 anti-HPV 6, anti-HPV 11, anti-HPV 16 and anti-HPV 18 responses that were comparable to those observed in women who received a standard 0, 2 and 6 month vaccination regimen (see Dosage and Administration).

During clinical trials, 2,266 women (vaccine = 1,115 versus placebo = 1,151) reported at least one pregnancy. Overall, the proportions of pregnancies with an adverse outcome were comparable in subjects who received Gardasil and subjects who received placebo.

Further subanalyses were done to evaluate pregnancies with estimated onset within 30 days or more than 30 days from administration of a dose of Gardasil or placebo. For pregnancies with estimated onset within 30 days of vaccination, five cases of congenital anomaly were observed in the group that received Gardasil compared to zero cases of congenital anomaly in the group that received placebo. Conversely, in pregnancies with onset more than 30 days following vaccination, ten cases of congenital anomaly were observed in the group that received Gardasil compared with 16 cases of congenital anomaly in the group that received placebo. The types of anomalies observed were consistent (regardless of when pregnancy occurred in relation to vaccination) with those generally observed in pregnancies in women 16 to 26 years of age.

Thus, there is no evidence to suggest that administration of Gardasil adversely affects fertility, pregnancy or infant outcomes.

References
(1) Human papillomavirus vaccine, recombinant (Gardasil), Merck Sharpe & Dohme (Aust.) Pty Ltd. MIMSOnline. Last updated: 27/7/2007

Regards.