The armed man is holding doctors hostage at the Cerrahpasa Tip Fakultesi Hospital
The man is believed to be a patient who was in the psychiatric unit at the Cerrahpasa Tip Fakultesi Hospital, the Istanbul University Hospital.
Several doctors as well as hospital staff are believed to be among those being held.
Police have been sent to the scene in the centre of the Turkish capital.
A policeman told Hurriyet news the patient pointed a gun at his own head before locking himself in a room and threatening to shoot some translators.
Police are currently negotiating with the patient to convince him to leave the room safely.
The news comes as Turks are on edge a month after Islamic State (ISIS) jihadis attacked the popular upmarket Reina nightclub on the shores of the Bosphorus in central Istanbul.
A total of 39 people were killed and at least 70 were injured in the incident after gunman Abdulkadir Masharipov entered the nightclub and started shooting.
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