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Chowdhury handed over his resignation letter to parliament Speaker Jamiruddin Sircar who will officiate as the president till a successor is chosen within 90 days.
Shortly before leaving Banga Bhavan, the presidential palace, Chowdhury, 70, told reporters, "I have resigned to uphold parliamentary democracy and show respect to the BNP Parliamentary Party", which had on Thursday night asked him to quit citing lack of confidence.
This is the first time in Bangladesh, which became independent 31 years ago, that an elected president was forced to quit by the same ruling party, which had ensured his election to the highest post less than eight months ago.
BNP MPs had attacked Chowdhury for not visiting the grave of Ziaur Rahman, who ruled Bangladesh for seven years after seizing power in 1975, on his death anniversary on May 30 last.
Rahman was assassinated in a military coup in 1982.
The MPs also criticised Chowdhury for not mentioning in his official message on the occasion, the contribution of Ziaur Rahman to Bangladesh's liberation war.
Sources close to Chowdhury said he would return to the medical profession.
Bangladesh's two main political groups - the BNP led by Prime Minister Khaleda Zia and the opposition Awami League led by former prime minister Sheikh Hasina - are sharply divided on who first proclaimed independence when the country broke away from Pakistan in 1971.
While BNP says Ziaur Rahman, then a major in the Pakistani army, declared independence on March 26, 1971, the Awami League says Sheikh Mujibur Rahman, father of Sheikh Hasina, declared independence.
The latter version of events is the universally accepted one.
The Awami League termed Chowdhury's virtual ouster as 'undemocratic' and a 'threat' to the parliamentary system of governance.
Chowdhury's resignation came shortly after the Awami League decided to end its eight-month-old boycott of parliament after a meeting of its top policy-making body Central Working Committee.
Former military dictator and head of the opposition Jatiya Party H M Ershad, who grabbed power soon after Ziaur Rahman's assassination, termed Chowdhury's removal as 'exceptional' in the country's political history.
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