In 2008, CDC published a supplement to the journal Cancer describing incidence patterns of human papillomavirus (HPV)-associated cancers prior to availability of an HPV vaccine. This report updates the information on HPV-associated female genital cancer incidence with more recent data, adds information on trends, and includes American Indian/Alaska Native (AI/AN) populations. We used combined data from two federal cancer surveillance programs, CDC's National Program of Cancer Registries (NPCR) and NCI's Surveillance, Epidemiology, and End Results (SEER) Program, covering 92% of the U.S. population from 1999 to 2004, to examine recent trends and incidence of invasive cervical carcinoma and vaginal and vulvar squamous cell carcinoma (SCC). Incidence of in situ vaginal and vulvar SCC are also presented. The average annual age-adjusted rate of cervical cancer among women of all races/ethnicities was 8.5/100,000. Annual cervical cancer incidence rates were highest but declined more rapidly among Hispanic and black women compared with non-Hispanic and white women. The rate of vulvar cancer among all women was 1.7/100,000 and was higher among white women than other racial groups. Vulvar cancer rates rose among black women (+2.9% per year) and were relatively stable among all other racial and ethnic groups over the 6-year period. Vaginal cancer was rare (rate 0.5/100,000); the rate was higher among black women than other racial groups and higher among Hispanic women than among non-Hispanic women. A significant decline of vaginal cancer was observed only among black women (-6.2% per year). This article confirms previous findings on racial disparities in HPV-associated female genital cancers. Any post-HPV vaccine declines in these cancers should be interpreted in light of current declines. Enhancing current cancer surveillance systems, combined with special studies to collect data on in situ or precancerous lesions of these cancers, will provide important information in determining the potential impact of the HPV vaccine.