BACKGROUND The Say-Barber-Biesecker-Young-Simpson (SBBYS) variant of Ohdo syndrome is characterized by congenital hypothyroidism, facial dysmorphism, postaxial polydactyly, and mental retardation. The SBBYS variant of Ohdo syndrome is extremely rare with only 19 cases previously reported in the literature. A case is presented of chronic otitis media associated with cholesteatoma in a six-year-old boy with the SBBYS variant of Ohdo syndrome. CASE REPORT A 6-year-old boy presented with perforation of the tympanic membrane and a cholesteatoma in the mesotympanic-attic region associated with chronic otitis media. The child had previously been diagnosed with the SBBYS variant of Ohdo syndrome. Following computed tomography (CT) and magnetic resonance imaging (MRI), tympanoplasty was performed with removal of the lesion. CONCLUSIONS This is the first case described in the literature of chronic otitis media associated with cholesteatoma in a patient with the SBBYS variant of Ohdo syndrome. This case demonstrates the importance of specialist otolaryngology referral for patient management.