The violence erupted yesterday after activists protesting against the Islamists' policies and targeting of journalists, marched to the building guarded by police and Brotherhood members.
More than 120 people were hurt as hundreds of opposition activists and the Islamists battled in the streets of the Mokattam neighbourhood where the headquarters are situated.
Thousands of Brotherhood supporters had travelled in front of the headquarters since Thursday to protect the building.
The protesters torched their buses to keep them from returning to their home towns.
Meanwhile, the police are attempting to create a buffer zone between the two sides in order to minimise injuries and prevent casualties.