Lowe syndrome is an X-linked recessive inheritance disease characterized by congenital cataracts, intellectual disability, and renal failure. We report a case of Lowe syndrome associated with congenital missing teeth, impacted teeth, and dentigerous cysts. The patient was a 16-year-old boy seen for pediatric dental management. A panoramic radiograph showed numerous lesions, including missing bilateral mandibular first and second premolars, impacted maxillary bilateral canines and left second premolar, and radiolucent lesions around both mandibular third molars. Based on computed tomographic findings, the radiolucent lesions were suspected to be dentigerous cysts or keratocystic odontogenic tumors. With the patient under general anesthesia, bilateral extraction of the mandibular third molars and extirpation of the cysts were performed. The pathological diagnosis of both lesions was dentigerous cysts. The postoperative progress was good, but expansion of radiolucent areas was detected around both maxillary third molars 2 years after the operation. Bilateral extraction of the maxillary third molars was performed with the patient under general anesthesia. The pathological findings led to the diagnosis of hyperplastic dental sacs as opposed to dentigerous cysts. There have been no clinical or radiographic signs of cyst recurrence and no change in the position of the unerupted teeth during 5 years of follow up.