There are at least 120 completely characterized human papillomavirus (HPV) types and putative new types are continuously found. Both squamous cell carcinoma of the skin (SCC) and other skin lesions commonly contain multiple cutaneous HPV types. The objective of this study was to achieve an improved resolution of the diversity of HPV types in lesions such as SCCs, actinic keratoses (AKs) and keratoacanthomas (KAs). Fresh frozen biopsies from 37 SCC lesions, 36 AK lesions and 92 KA lesions and swab samples from the top of the lesion from 86 SCCs and 92 AKs were amplified using the general HPV primers FAP and mixed to three pools followed by high throughput sequencing. We obtained 2196 reads with homology to HPV. In the pool of SCC/AK biopsies 48 different HPV types were found. Eighty-three types were found in the pool of SCC/AK swab samples and 64 types in the KA biopsies, respectively. For 9 novel putative HPV types most of the amplimer sequence was obtained, whereas for an additional 35 novel putative HPV types only partial amplimer sequences were obtained. Most of the novel putative types belonged to the genus Gamma. In conclusion, high throughput sequencing was an effective means to identify both known and previously unknown HPV types in putatively HPV-associated lesions and has revealed an extended diversity of HPV types.