Background: Human papillomavirus (HPV) is diagnosed in most cervical cancers and is the fourth cause of cancer worldwide. Currently, fourteen HPV types are considered carcinogenic (HPV 16/18/31/33/35/39/45/51/52/56/58/59/66/68) with different oncogenicity. Cervical lesions might be due to HR (high risk)-HPV for what is important to identify new methods to genotype cervical lesions. The main goal was to identify, for the first time, HPV-HR in cervical lesions using Anyplex™ Detection kit in paraffin-embedded tissue. (2) Methods: It was performed a retrospective study in 45 women from Academic Hospital of Cova da Beira (CHUCB). DNA extraction was performed and through Anyplex™ II HPV-HR Detection kit HPV-HR were genotyped. (3) Results: HPV-HR were identified in 38 women; HPV-16 (55,26%), HPV-18/39/56/58/59 (5,26%), HPV-31 (21,05%), HPV-35 (7,89%), HPV-51/6 (2,63%) and HPV-52 (10,53%). (4) Conclusions: Our results reflect that Anyplex™ II HPV-HR Detection kit, designed for HR-HPV genotyping of cervical cancer screening, might be properly used to HR-HPV genotyping in histology. The proposed methodology allows an easy and cheaper technique that should be used as a future cervical risk stratification. It is a strong tool to be implemented in clinical practice in order to detect HR-HPV detection in cervical lesions, contributing to a more accurate diagnosis.