Background Condylomata acuminata - genitals warts - are benign squamous epithelial lesions involving the skin and/or mucosa of the anogenital region, which are typically associated with low-risk human papillomavirus (lrHPV) infection and only exceptionally undergo malignant transformation. In contrast to small lesions, giant condylomata acuminata [also known as Buschke-Löwenstein tumors (BLT)] are locally aggressive and associated with invasive squamous cell carcinoma (SCC) in approximately 50% of cases. While most reported cases of SCC arising in BLT are associated with high-risk HPV infection and/or immunosuppression [i.e., human immunodeficiency virus (HIV) infection, etc.], our group has recently encountered a series of cases associated with lrHPV infection from immunocompetent patients. Design In-house cases at a single large academic institution between 2013 and 2024 were identified prospectively at sign-out and retrospectively using the surgical pathology records database. Clinical-grade RNA in situ hybridization was used to confirm the presence of transcriptionally active lrHPV subtypes in the SCC. Clinicopathologic information was manually extracted from the electronic medical record system. Representative normal and SCC tissue blocks for each case were selected for HPV DNA analysis using hybrid capture-based next-generation sequencing (NGS) with the Twist Biosciences Comprehensive Viral Research Panel (CVRP) -- which targets 143 HPV subtypes -- and whole-exome sequencing (WES) using the Twist Biosciences Exome 2.0 Panel. Results Four cases of lrHPV-associated SCC arising in a BLT were identified (clinicopathologic information provided in the Table). A majority of the patients (75%) were male and current/former tobacco users. Three of the patients had a long-standing (20+ year) history of condylomata, and the median size of the BLT/SCC mass was 9.75 cm. Based on HPV capture sequencing, all SCC harbored only HPV6 DNA. WES revealed a variety of oncogenic alterations across the tumors, including: TP53 hotspot mutations (n = 2); CDKN2A and LATS1 stop-gain mutations (n = 1); KDM5C, NFE2L2, and STAT3 missense mutations (n = 1); and, a NOTCH2 frameshift mutation (n = 1). All tumors demonstrated genomic complexity, including aneuploidy, copy-neutral loss of heterozygosity, and/or focal gains and losses [i.e., KMT2B two-copy loss (n = 1)]. Case Sex Age (years) Current/Former Tobacco Use Tumor Site Size (cm) HPV Capture Somatic Variants Copy Number Alterations S01 M 60 No Penis 9.0 HPV6 CDKN2A p.R80X KDM5C p.E698K Copy-neutral LOH of 9p24.3-p21.1 S02 F 49 Yes Urethra/urinary bladder 7.5 HPV6 TP53 p.C238S LATS1 p.R744X NFE2L2 p.W24C Copy-neutral LOH of 6q23.3-q27 and 17p13.3-p13.1 S03 M 37 Yes Skin of pubis/scrotum 12.7 HPV6 STAT3 p.T716M NOTCH2 p.C996fs Aneuploidy KMT2B two-copy loss S04 M 48 Yes Perineum 10.5 HPV6 TP53 p.P151T Aneuploidy Copy-loss of 17p13.3-p13.1 LOH = loss of heterozygosity Conclusions A subset of SCC arising in BLT are associated with lrHPV infection but also harbor somatic oncogenic variants and demonstrate genomic complexity.