Cystinosis is a multisystemic genetic storage disorder characterized by a mutation in the transporter system of cystine. The disease particularly affects the renal system by causing deposition of cystine crystals leading to, if untreated, Fanconi syndrome and end-stage renal disease. This disease also affects the ocular system, central nervous system, endocrine system, hepatobiliary system, and musculoskeletal system. We present the first case of cystine crystal deposition within an odontogenic cyst, confirmed by the correlation of the clinical, radiographic, and histologic findings on this patient.