OBJECTIVE To audit the uptake of pandemic (H1N1) 2009 influenza vaccine in pregnant women entering the 2010 influenza season in Western Australia, and to identify why some women did not receive the vaccine. METHODS Cross-sectional study of consecutive patients attending the Joondalup Health Campus public antenatal clinics in WA in January 2010. METHODS Audit of uptake of the H1N1-specific vaccine. METHODS Rate of H1N1-specific vaccination, and reasons for not being the vaccinated. RESULTS 479 of 541 women who attended the clinics (88.5%) were included in the audit. Three women had been infected with pandemic influenza in the preceding influenza season, leaving 476 women who were eligible for vaccination in pregnancy. Of these 476 women, only 33(6.9%) had been vaccinated. Of the remaining 443 women who were eligible to receive the vaccine but had not been vaccinated, 63.9% had not been offered vaccination despite multiple visits to their general practitioners during pregnancy, 19.6% had been advised by their GPs against vaccination in pregnancy, and 61.6% stated that they would decline vaccination if offered because of safety concerns. CONCLUSIONS Uptake of H1N1-specific influenza vaccine in pregnant women was poor. Reasons for this relate both to vaccination not being offered to or actively sought by the women, as well as concerns - of both the women and their GPs - about vaccine safety in pregnancy. Uptake in this setting may improve if vaccination is offered through public antenatal clinics with concurrent safety education for obstetricians and vaccination providers.