Abu Zayd came to the public eye in 1995 when Islamist lawyers filed suit against him, demanding he divorce his wife because his writings insulted Islam. The couple refused a court order to divorce and fled Egypt for fear of being attacked by Muslim fundamentalists.
The case outraged secular Arab intellectuals, who saw it as an attack on freedom of expression.
Abu Zayd later appealed the ruling and won but remained abroad, spending most of the last 15 years in the Netherlands.
Born in 1943 in a village north of Cairo, Abu Zayd obtained a doctorate in Islamic studies in 1981 and took a job teaching Arabic studies at Cairo University a year later.
Instead of the traditional literal interpretation of the Koran, Abu Zayd used contemporary methodology, including linguistics, to interpret Islam's holy text.
His writings on the Koran, especially his renowned book "A Critique of Religious Discourse," drew the wrath of Muslim fundamentalists, who accused Abu Zayd of questioning the text's divine origins and therefore of being an unbeliever.
In a 2000 interview, he said: "I would like to tell the Muslim nation that I was born, raised and lived as a Muslim, and, God willing, I will die as a Muslim."
He is survived by his wife, Ibtihal Younes, who lectures on French literature at Cairo University.