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Highlights • Perineal inclusion cysts may harbor clinically occult malignant degeneration. • Histological analysis of large inclusion cysts required to rule out occult malignancy. • Perineal cysts with malignant degeneration are diagnostic, reconstructive challenge. • Risk of malignancy in perineal inclusion cysts helps treatment decisions. • Large perineal cyst requires multidisciplinary surgical team for excision and closure. • Colostomy as adjunct of perineal reconstruction after excision of inclusion cyst. • Perineal inclusion cysts may present as atypical, cavitating lesions., Introduction Cutaneous squamous cell cancer (cSCC) is a common condition, with straight forward and well-known heuristics regarding diagnosis, treatment, and surveillance. cSCC arising in an epidermal inclusion cyst is rare, but not unheard of. In contrast, the authors’ are unaware of any prior reports of cSCC arising in an epidermal inclusion cyst within an atypical cavernous and cavitating lesion in the perineum. Presentation of case A 48-year-old male presented with a cavitating and rapidly growing cutaneous perineal lesion. Preliminary diagnostic procedures (biopsy) showed benign pathology and imaging showed no involvement of perineal organs such as prostate or rectum. Discordance between initial diagnostics and clinical features prompted multi-specialty consultation, including dermatological pathology. Repeat biopsy yielded in situ, possibly invasive squamous cell cancer, arising in the background of an epidermal inclusion cyst. Wide excision with advancement flap reconstruction was employed, with temporary diverting colostomy to avoid perineal sepsis. Discussion Location and appearance of this lesion provided a diagnostic and treatment challenge requiring multi-specialty involvement for diagnosis and successful treatment. Specialists from urology, general surgery, dermatology, general and dermatological pathology, plastic and reconstructive surgery, colorectal surgery and medical and radiation oncology were involved in diagnosis, treatment plan and execution. None of the specialists involved had seen this singular presentation before, and this created an ownership and management challenge. Conclusion The cavitating, atypical appearance of lesion complicated diagnosis. Location required pre-treatment coordination and deliberation between dermatology, urology, general surgery, and plastic surgery. Malignant degeneration of inclusion cysts, although rare, has to be kept in mind, especially when presenting with rapid growth, and persistence in ruling out malignant diagnosis is fundamental.