Hoodbhoy remains one of Pakistan's most prominent academics. He is the author of "Islam and Science: Religious Orthodoxy and the Battle for Rationality" He is the head of "Mashal" Books in Lahore, which claims to make "a major translation effort to produce books in Urdu that promote modern thought, human rights, and emancipation of women". Hoodbhoy has written for "Project Syndicate", "DAWN", "The New York Times" and "The Express Tribune". Hoodbhoy is generally considered one of the most vocal, progressive and liberal members of the Pakistani intelligentsia. His daughter, Alia Amirali, is also a well-known feminist and political activist.