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Purpose Conjunctival papillomata are squamous epithelial tumors with a strong association with human papilloma virus (HPV) types 6 and 11. They are benign conjunctival tumors that can be treated by surgical excision. We report a case where topical immunosuppressive therapy modified the local T-cell immunity in the conjunctiva resulting in papilloma development in a patient with keratoconus and a strong atopic history. Methods A case report of a 44-year-old man with a history of severe ocular and generalized atopy is presented. We present the problems encountered in management of his severe ocular allergy and how these impeded the management of his keratoconus. Results Conventional antiallergy topical medication was not producing symptom relief in this patient, and so topical immunosuppression was commenced using ciclosporin ointment 0.2%. This therapy modified the local T-cell immunity in the conjunctiva resulting in the development of papillomata which contributed to the intolerance of contact lens wear for visual rehabilitation of the keratoconus in the patient. These lesions were surgically removed but typically recurred and required further surgical excision. Adjunct cryotherapy was also performed at the time of the surgery to try to stem the recurrence of the papillomas. Conclusions To the best of our knowledge and following a review of the published literature using key databases that include Medline and PubMed, this is the first report confirming the development of conjunctival papillomas secondary to HPV type 6 in a ciclosporin-treated patient.