According to Jihad is the way by Mustafa Mashhur Leader of the Muslim Brotherhood in Egypt, 1996-2002 
It should be known that jihad and preparation towards jihad are not only for the purpose of fending off assaults and attacks of Allah's enemies from Muslims, but are also for the purpose of realizing the great task of establishing an Islamic state and strengthening the religion and spreading it around the world.
Jihad for Allah is not limited to the specific region of the Islamic countries, since the Muslim homeland is one and is not divided, and the banner of Jihad has already been raised in some of its parts, and shall continue to be raised, with the help of Allah, until every inch of the land of Islam will be liberated, and the State of Islam established.
The problems of the Islamic world - such as in Palestine, Afghanistan, Syria, Eritrea or the Philippines - are not issues of territories and nations, but of faith and religion.They are the problems of Islam and all Muslims, and their resolution cannot be negotiated and bargained by recognizing the enemy's right to the Islamic land he stole, and therefore there is no other option but jihad for Allah, and this is why jihad is the way.
U.S. White House counterterrorism chief Juan Zarate, who says "The Muslim Brotherhood is a group that worries us not because it deals with philosophical or ideological ideas but because it defends the use of violence against civilians."
Links to violence
The Brotherhood is widely believed to have had a "secret apparatus" responsible for attacks in Egypt, including the assassination of Mahmoud an-Nukrashi Pasha, the Egyptian Prime Minister in 1948 and the president of Egypt in 1981
Rachel Aspden's article, The Rise of the Brotherhood states that The Muslim Brotherhood currently advocates suicide bombing attacks on civilians to fight Zionism, and its self-admitted Palestinian wing Hamas indiscriminately targets Jews as such, both civilians and the military, in Israel. In its Charter, Hamas cites The Protocols of the Elders of Zion and prophesizes the ultimate complete annihilation of Jewry.
Newsweek journalists Mark Hosenball and Michael Isikoff reported connections between al-Qaeda and Brotherhood figures Mamoun Darkazanli and Youssef Nada.
A similar article in the Financial Times reported financial links between 74-year-old Swiss Muslim convert, and businessman Ahmed Huber, and members of the Muslim Brotherhood, notably Youssef Nada, Ali Ghaleb Himmat. According to the U.S. government, Al Taqwa "has long acted as financial advisers to al-Qaeda." Huber is noted in Europe for his links with alleged neo-Nazi and other far right elements. He is reported to have "confirmed" having "had contact with associates of Osama bin Laden at an Islamic conference in Beirut," whom he called `very discreet, well-educated, very intelligent people.`
Abdul Rahman al-Amoudi was an influential lobbyist and founder and head of the Brotherhood-linked American Muslim Council before being convicted and sentenced to 23 years in prison for conspiracy to murder Saudi Prince Abdullah at the behest of Libyan leader Muammar al-Gaddafi.
Muslim Brotherhood - Wikipedia, the free encyclopedia