Early in 2006, Amer was expelled from al-Azhar University, Damanhour Campus, for criticizing some of the university's conservative instructors, writing in his blog that the "professors and sheikhs at al-Azhar who .. stand against anyone who thinks freely" would "end up in the dustbin of history".
University administrators also filed a communiqué to the Public Prosecutor Office against their former student, alleging he was "spreading rumours endangering public security" and "defaming President Mubarak".