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Each Estonian prison accommodates a chapel and working chaplains. This enables prisoners to adhere to their religious beliefs and customs while imprisoned. Chaplains help ensure in prison religious freedom as a fundamental right. Chaplains support prisoners in their religious needs and assist them on their way to society.

The Chaplain Service is organized in cooperation of the Estonian Council of Churches and the state and operates in the spirit of collaboration of churches and religions. In their daily work, chaplains meet prisoners that subscribe to different churches and religions and help them resolve issues related to topics such as pastoral care, religious services, religion related diet, holidays, religious symbolism, and literature. Thereat, chaplains consider religious needs and freedom of religion of all prisoners, to that end cooperating with ministers of different churches and religions as well as with other volunteers.

Prisoners may see the chaplain regularly and participate in church services and religious events. The two main domains of religious activity in prison are individual pastoral care and participation in religious services and other religious ceremonies. Important religious ceremonies, for example, include confession and the Holy Communion as well as baptism and confirmation. Every now and then, the chaplain leads a marriage ceremony in prison. Prisoners can gain further religious knowledge in classes of Religious Studies and Confirmation Studies.  

Chaplains participate in prisoners’ return to society, implementing religious social programs and advising prisoners on issues related to religion and ethics. The chaplain also organizes reconciliation with the prisoners’ family and helps establish ties with a congregation or rehabilitation center which could provide prisoners with social support and certainty after their release from prison. The chaplain further coordinates prison-based activities of volunteers from different religious associations (see Volunteers in prison).