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Healthcare in prison is part of the state’s health care system. In the prison medical ward, prisoners receive general out-patient medical care and specialized medical care; in-patient treatment is also available in every prison. Prisoners that have tuberculosis are treated at Tallinn Prison’s specialized hospital in Maardu. If a prisoner requires treatment which the prison is unable to provide, the prisoner is transferred to a civilian hospital for medical care. Prisoners’ medical expenses are covered from the state budget through the Ministry of Justice.

All prisoners arriving in prison are subjected to an initial health check. This will determine any illnesses a prisoner may have (incl. infectious diseases such as tuberculosis, hepatitis, and HIV) and enable prescription of further treatment. All prisoners undergo a radiographic examination of the lungs upon placement in prison and once a year, moving forward.

HIV/AIDS prevention in prison is based on the Estonian National Health Plan 2009–2020. In all prisons, prisoners are tested and advised in relation to HIV upon arrival in prison; moving forward, a repeat test is administered once a year. Counselors are trained health care professionals.

For its good work in providing health care services, the World Health Organization has given the Prison Service a number of awards for best practice. The latest best practice award was received by Harku Prison in 2011.

As from 2010, prison medical wards and hospital are connected to the Health Information System.