Born on July 5, 1948, at Kongandoor (Punnathura Parish), Joseph (Babychan) had his education in St. Thomas L. P. School Kongandoor, St. Joseph's High School, Punnathura and St. Berchmans' College, Changanacherry. Completing his seminary studies at St. Thomas Minor Seminary, Changanacherry and St.Thomas Apostolic Seminary, Vadavathoor, Kottayam, he was ordained priest on 18 December 1974 by Archbishop Mar Joseph Powathil, then auxiliary bishop of Changanacherry. After his ministry as assistant parish priest for a few years he was appointed Director of Sandesanilayam, the Catechetical and Pastoral Centre of the Archeparchy, in 1979 and the Chaplain of Christian Workers' Movement of the Archeparchy. In the Catechetical field, he introduced many training programmes, including Catechetical Leaders' Training (CLT), which is being continued to this day by Sandesanilayam. In 1983 he was sent for higher studies at Gregorian University Rome, where he took doctorate in Church History. Back from Rome, in 1989 he was appointed professor in St. Thomas Apostolic Seminary, Vadavathoor and Missionary Orientation Centre, Manganam, Kottayam and Vicar of St. Sebastian's Church, Kodinattumkunnu. During this period he was instrumental in starting Marthoma Vidyanikethan, the Higher Institute of Religious Sciences for the Laity, at Changanacherry, with the active support of Archbishop Mar Joseph Powathil. This Institute is a unique venture sponsored by Paurastya Vidyapitam, Vadavathoor, conferring P.G. degree recognized by the Congregation for Catholic Education, Rome and Rev. Dr. Joseph Perumthottam has been at its helm for a decade. Simultaneously he was the vicar of Mar Sleeva Church, Ponga. He also served as the Secretary of the Pastoral Council, Presbyteral Council, Director of the Liturgy Department, member of the Central Liturgical Committee and Board member of Liturgy Research Centre (LRC), Kakkanad. He was nominated auxiliary bishop on 24 April 2002 and was ordained bishop by Archbishop Mar Joseph Powathil at St Mary's Metropolitan Church, Changanacherry, on 20 May 2002, the 116th anniversary of the Archeparchy.

On 19 March 2007 he succeeded Archbishop Mar Joseph Powathil as the Archbishop of Changanacherry and was enthroned by His Beatitude Mar Varkey Vithayathil at a solemn function held at the Metropolitan Church ground, Changanacherry.

Later a small portion among them became reunited to Catholic faith and they now form the Syro-Malankara Church. The majority of the Thomas Christians who always remained faithful to the Catholic faith are the present Syro-Malabar Church.

Archbishop Mar Joseph Perumthottam has been shepherding the eparchy on the solid foundation laid by his predecessor. He envisages six important areas of pastoral ministry, namely Liturgy, Faith formation, Education, Social Welfare and Health Care, Solidarity and Communion and Mission Work. Primacy is always given to ensure a sound ecclesial life and liturgical spirituality in the Archeparchy. Regular parish pastoral visits, faith formation through "Kudumbakoottaymakal", insistence on the significance of lay leadership, special care for the migrants from our eparchy, determined efforts to eradicate social evils like alcoholism etc. are some of the major features of his pastoral vision.

Pope Leo XIII of happy memory by his Bull 'Quod Jam Pridem' dated May 20, 1887 established two Vicariates Apostolic - Kottayam and Thrissur - exclusively for the Syro-Malabarians and Dr. Charles Lavigne and Dr. Adolph Medlycott respectively were appointed the Vicars Apostolic.

He has been a member of CBCI Standing Committee and the Permanent Synod of Syro-Malabar Church since 2007. He has been working as the member and chairman of various Commissions of KCBC and Syro-Malabar Synod. In December 2013 he was elected as the vice-president of KCBC. In August 2014 he was selected as the Chairman of the Synodal Commission for Vadavathoor Seminary and the Vice Chancellor of Paurastya Vidyapitham.

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