From the Anti-defamation League
Profile: Egypt
"Anti-Semitism in the Muslim/Arab World
Profile: Egypt’s Muslim Brotherhood
The overthrow of Hosni Mubarak's regime by the Egyptian people in February 2011 marks a turning point in the political development of the Muslim Brotherhood, the country's largest and best organized religious, social and political movement. Since the upheaval, the Brotherhood has sought to quickly assert its influence and define the role it will play in Egypt's post-revolutionary political system. On June 24, 2012, one of the Brotherhood's very own leaders, Mohamed Morsi, was elected president of Egypt.
Although the group has vowed to promote peaceful co-existence and stability within Egypt by means of fostering better relations between Muslim and Christian citizens, the Brotherhood's leadership continues to articulate its historical and ideological opposition to the existence of the State of Israel and to the 1979 Camp David peace accord between the two countries."
The full report includes this statement on Israel from FJP's [Muslim Brotherhood's political arm] official political program:
"The issue of Palestine is the most important issue of Egyptian national security, in addition to being an Arab or Muslim cause, because the Zionist Entity is a racist colonizing expansionist entity, possessing weapons of mass destruction, which has caused the outbreak of many wars in the region, affecting the geographical, political, social and economic situation, disrupting development programs and displacing people from their homes, in addition to the acquisition of Islamic and Christian holy places in Palestine. Therefore the party sees the need to make all efforts to resolve this issue and ensure the rights of Palestinian self-determination and the return of refugees to their homes, establish their state and its capital Jerusalem, restore all the holy places of Muslims and Christians in Palestine and the evacuation of the entire region(Middle East) of weapons of mass destruction."
ADL Welcomes Resignation of Morsi Adviser who Called for Jews to ‘Leave Israel’
New York, NY, January 7, 2013 … The Anti-Defamation League (ADL) today welcomed the resignation of a close adviser to Egyptian President Mohammed Morsi who last week called for Jews of Egyptian descent to return to Egypt and “leave Israel.”
The official, Essam al-Erian, also reportedly referred to Israel as a “brutal, bloody and racist” state that was guilty of “war crimes against humanity.” He predicted the Jewish state would disappear within a decade. Al-Erian is the deputy head of the Muslim Brotherhood’s Freedom and Justice Party. According to news reports, he submitted his resignation as a presidential adviser earlier today.
“We welcome the resignation of Essam al-Erian,” said Abraham H. Foxman, ADL National Director. “We hope that President Morsi and other Egyptian government leaders will now make it clear that the defamation of Israel and Jews has no place in the country’s national dialogue.”
Although the Brotherhood includes anti-Jewish elements and favor the Palestinian position regarding Israel, I haven't seen any evidence that they persecuted Jews while in power or did anything else justifying mass murder and imprisonment of their members.
