Egypt's military-installed authorities are engaged in a deadly crackdown against the Islamist movement, which swept elections in Egypt after the overthrow of president Hosni Mubarak in 2011 but is now blacklisted as a "terrorist group."
A court in the Mediterranean city of Alexandria ordered authorities to bar any candidacies from Brotherhood members or former members in presidential and parliamentary elections.
The ruling came after a group of private citizens who have protested against the Brotherhood filed a petition calling for the ban.
"We submitted videos, photos and documents showing terrorist acts carried out by the Muslim Brotherhood, which is why it is illogical that they lead the country or represent its people in elections."
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In December, the authorities blacklisted the Muslim Brotherhood as a "terrorist group" after blaming it for a deadly bombing north of Cairo that was claimed by a jihadist group.
Former army chief Abdel Fattah al-Sisi, whose popularity has soared since he deposed Morsi last summer following massive protests, is widely expected to win the May 26-27 presidential election, which is to be followed by parliamentary polls.
More than 15,000 Islamists, mainly Brotherhood members, have been jailed, while hundreds have been sentenced to death following often speedy trials.
The 85-year-old Brotherhood, Egypt's most well-organised opposition group during decades of dictatorship despite being banned, stepped out of the shadows after the 2011 uprising.
It won a string of polls culminating in the 2012 presidential election, when its candidate Morsi became Egypt's first freely elected leader.
Under Mubarak's rule, the group was banned but tolerated, and had candidates run as independents. In 2005 Brotherhood candidates won dozens of seats in parliament.
Key leaders of the group have been based in London since the toppling of Morsi and the police crackdown.
Today's court ruling against the Brotherhood came hours after a bomb attack in an upmarket central Cairo district wounded two policemen and a passer-by.