We present a case of Brooke-Spiegler syndrome with a germline deep intronic mutation in the CYLD gene leading to intronic exonization. Additionally, diverse somatic mutations were identified, namely loss of heterozygosity, a recurrent nonsense mutation, and a sequence mutation causing exon skipping. These somatic aberrations were identified in 4 different cylindromas that had been removed from the patient. Additionally, we microscopically studied a spiradenocylindroma that showed unusual histology, including foci of follicular differentiation. A deep intronic mutation resulting in exonization and a somatic sequence mutations causing exon skipping are hitherto unreported genetic mechanisms involving the CYLD gene in patients with Brooke-Spiegler syndrome.