Skin warts are ubiquitous, self-limiting, benign neoplasms caused by human papillomaviruses (HPV). Several studies have investigated the prevalence and diversity of HPV types in the three main types of skin warts: common, plantar, and flat warts. Using different methodological approaches and diverse populations, several HPV types were detected in skin warts, but often the etiological link remained unconfirmed. This review addresses recently improved multiple strategies for investigating the presence of HPVs in skin warts, covering proper sampling techniques for HPV testing, choice of molecular method(s) for HPV detection, and assignment of the etiological causality of the tested skin wart to a causative HPV type using cellular viral load estimation. These novel approaches provide useful insight into the range of HPV types causing skin warts and support a refined understanding of their etiology. In addition, we conducted a literature review of the main studies examining HPV prevalence and genotype distribution in common warts, plantar warts, and flat warts. Finally, HPV type-specific histopathological patterns in skin warts are briefly discussed.