Objective: Human papillomavirus (HPV) infection is a global public health concern and associated with cervical cancer. HPV genotype mapping has an essential role in prevention and control strategy in developing more suitable HPV vaccine for Indonesia. Methods: This was a descriptive retrospective cross-sectional study from 2012 until 2022 at Kalgen Laboratory, Jakarta from all over the metropolitan regions. The total 76,413 samples were collected with consecutive sampling, which 694 excluded, thus final samples used were 75,719. HPV DNA test was performed using the polymerase chain reaction (PCR): SPF10-DEIA-LiPA25 methods. HPV genotyping procedures included DNA extraction, PCR using the HPV XpressMatrix kit, and hybridization. Results: From 75,719 samples, 93.4% was negative for intraepithelial lesion or malignancy (NILM). Among 6.6% of total 75,719 samples of abnormal cytology groups, 53.8% were atypical squamous cells of undetermined significance (ASCUS), 32.9% were low grade intraepithelial lesion (LSIL), and 13.3% were high grade intraepithelial lesion (HSIL). The most common high risk HPV genotypes among HSIL were 16, 18, 52, 58, 33, 51, and 53. Single HPV infection was more common compared to multiple infections. Conclusion This study showed that HR-HPV types among HSIL were 16, 18, 52, 58, 33, 51, and 53. HPV 52 was the most frequent type among NILM, ASCUS, and LSIL. Thus, it could serve as a potential future reference to create a more suitable HPV nonavalent vaccine for Indonesian population based on its different epidemiology.