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Mucinous metaplasia of the squamous epithelium of the glans penis is very rarely seen in the setting of Zoon’s balanitis. We report a case of 40 year old male with a past medical history of paroxysmal nocturnal hemoglobinuria, status-post allogeneic hematopoietic cell transplantation from an HLA-matched sibling 6 years prior to evaluation, complicated by oral and cutaneous chronic graft-versus-host disease. Mucinous metaplasia was confirmed by PAS and Mucin stains, and plasmacytosis was confirmed by immunohistochemistry for CD138 and MUM1 markers. Kappa and Lambda immunostains revealed a polyclonal pattern. The etiology of zoon’s balanitis as well as the significance of mucinous metaplasia in these setting are unclear and need to be further investigated.