Opener Javed Omar, batsmen Mushfiqur Rahim, Tushar Imran and all-rounder Alok Kapali were omitted from the final squad announced today.
Habibul Bashar, who missed six matches against Zimbabwe and Kenya in July and August due to a thumb injury, has been retained as captain, though he was yet to recover fully.
''Mehrab Hossain Jr had some very good performances over the last two years and we hope he can do something good in the Champions Trophy,'' chief selector Faruk Ahmed told a news conference.
Bangladesh will play Sri Lanka, West Indies and Zimbabwe in the qualifying phase of the Champions Trophy from Oct. 7-14.
The top two teams will qualify for the main competition from October 15 to November 5.
Squad: Habibul Bashar (captain), Shahriar Nafees (vice-captain), Khaled Mashud, Mohammad Rafique, Mohammad Ashraful, Mashrafe Mortaza, Rajin Saleh, Abdur Razzak, Aftab Ahmed, Syed Rasel, Shahadat Hossain, Farhad Reza, Saqibul Hasan, Mehrab Hossain jnr.