There are no data on the incidence and persistence of high-risk human papillomavirus (HR-HPV) infections in female sex workers (FSWs). We aimed to describe and compare the rates of incidence and persistence of HR-HPV infections in FSWs and women from the general population (WGP) who attended healthcare facilities between May 2003 and December 2006 in Alicante, Spain. Women with an established HR-HPV infection at study entry were evaluated for the analysis of HR-HPV persistence, and those testing negative for HR-HPV infection at entry were evaluated for the analysis of incidence. HR-HPV infection was determined by the Digene HC2 HR HPV DNA Test. A total of 736 women - 592 WGP and 144 FSWs - were followed for a median of 16.8 months. Global incidence and persistence rates were 3.98 per 100 woman-years (95% confidence interval (CI) 2.91-5.45) and 26.81 per 100 woman-years (95% CI 20.08-35.79), respectively. In the multivariate analysis, only commercial sex work was associated with a statistically significant higher incidence (relative risk (RR) 4.72, 95% CI 2.45-9.09) and persistence (RR 1.93, 95% CI 1.08-3.46) of HR-HPV infection. Our data show that FSWs have both a higher incidence and a higher persistence of HR-HPV than WGP and should be prioritized in HPV-related cancer screening programs.