Human papillomaviruses from the beta genus (betaPV) are a possible cause of cutaneous squamous cell carcinoma (SCC). We assessed the extent to which betaPV infections persisted long-term in a subtropical Australian community and whether betaPV persistence is positively associated with actinic keratoses, precursor for SCC. Eyebrow hairs were collected from 171 participants of the community-based Nambour Skin Cancer Study in 1996 and 2003. Hair samples were tested for the presence of DNA from 25 different betaPV types and assessed in relation to actinic keratosis presence in 2007. In 1996, a total of 413 betaPV infections were found in 73% of participants, increasing to 490 infections among 85% in 2003. Of the total betaPV infections detected, 211 (30%) were found to persist. Age was significantly associated with betaPV persistence: those ages >60 years had 1.5-fold (95% confidence interval, 1.1-1.9) increased risk of type-specific viral persistence than those ages <40 years. After accounting for actinic keratoses at baseline, persistence of betaPV DNA resulted in a 1.4-fold (95% confidence interval, 1.0-1.9) increase in risk of having actinic keratoses on the face in 2007. In conclusion, persistent betaPV infections in this population were associated with an increased occurrence of actinic keratosis. Additional studies are needed to determine the possible association of betaPV persistence with SCC.