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Background: We analysed human papillomavirus (HPV) vaccination coverage from the 2007-2009 catch-up program for women aged 18-26 years by Division of General Practice (DGP), alongside a survey about under-notification. Methods: Coverage rates were calculated from the National HPV Vaccination Program Register. An online survey of immunisation coordinators in DGP assessed under-notification. Results: HPV vaccine coverage by DGPs varied greatly: dose 1, 22-70%; dose 2, 13-60%; dose 3, 7-49%. Most coordinators (38/52, 66%) believed that more than 80% of practices notified the register. Perceived notification barriers included being busy, not knowing how to notify, not obtaining consent, insufficient remuneration and delay in register establishment. Discussion: DGP coverage varied widely. Process barriers (time and resource limitations) probably contributed to under-notification, with informational barriers (unaware how to notify) and motivational barriers (not worth the effort) secondary to this. Differences in reported coverage between DGPs and states reflect both differences in notification rates and underlying HPV vaccine coverage.