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Metachondromatosis (MC) is a very rare genetic disease, which is infrequently reported worldwide, which leads to osteochondroma and enchondromatosis. The disease has been shown to be associated with loss of function of the tumor suppressor gene “protein tyrosine phosphatase, non-receptor type 11” (PTPN11).A 12-year-old female was admitted to the hospital with pain due to an enlarged mass in her left fifth finger.Examination of the left hand by computed tomography (CT) revealed an expanding type of round and low-density lesion in the fifth proximal phalanx. The patient then underwent technetium-99m methylene diphosphonate single-photon emission CT/CT (99mTc-MDP SPECT/CT) to assess the nature of the lesion. The SPECT/CT image revealed dilated osteopathy and increased activity of the fifth proximal phalanx on the left hand. Unexpectedly, the examination of the right hand revealed slight expanded lesions and increased activities of the third metacarpal and proximal phalange, as well as the fourth proximal phalange and the middle phalanx. On the basis of the patient's symptoms and the results of the above-mentioned examinations, we diagnosed the patient as having MC in her hands.Considering the pain of the fifth finger of the left hand, the patient underwent debridement of the fifth proximal phalanx of the left hand and internal fixation with bone graft taken from the body.The patient was discharged after a week of observation. One year later, she was admitted to the hospital again for removal of the bone healing internal fixation after osteoma surgery. Preoperative 99mTc-MDP SPECT/CT revealed that the left-handed lesions displayed postoperative changes, while the multiple lesions in the right hand increased in volume but remained unchanged in number.This case revealed the CT and 99mTc-MDP SPECT/CT imaging features of MC. Specifically, SPECT/CT imaging contributed to the diagnosis of clinically asymptomatic bone lesions, and the 3D SPECT/CT fusion allowed a more comprehensive and intuitive view of the lesion by combining anatomy and function.