A health ministry official said on Monday that test results ruled out any form of flu virus as a cause of death. At least 70 people have died from bird flu in Asia, but deaths have yet to be reported outside the region.
CNN-Turk television quoted the hospital as saying that the boy had died on Sunday of pneumonia.
Five other people, including three from his family, were being tested for bird flu. Initial test results showed that his two sisters and a brother were free of bird flu virus, while test results for two other patients have not yet been announced.
All patients were suffering from fever and pneumonia-like symptoms, doctors said. Turan Buzgan, a health ministry official, said: "The disease is not caused by bird flu or any other form of flu virus."
The boy had been on life support since his brain functions stopped when he died. He was among two brothers and two sisters between the ages of six and 15 who were admitted to hospital on Saturday after developing high fevers, coughing, and bleeding in their throats.
The children helped to raise poultry on a farm and were in close contact with sick birds. They became ill after reportedly eating one of them. The eldest sister was also reported to be in a critical condition.
Two other patients, aged five and 35, were sent to the same hospital on Sunday, the Anatolia news agency reported, as Turkish health and security authorities gathered to co-ordinate a response.
The Turkish authorities said last week that some chickens had tested positive for an H5 variant of bird flu and placed parts of an eastern town, Aralik, near the border with Armenia, under quarantine.
The sick brothers and sisters are from the town of Dogubeyazit, 60km south of Aralik.
Birds in Turkey, Romania, Russia and Croatia recently tested positive for the deadly H5N1 strain in birds, but no human cases have been detected.
Since 2003, the strain of bird flu has ravaged flocks of birds in Asia and killed at least 71 people there - most of them farm workers in close contact with birds.