INTRODUCTION
It depends on what you are claiming to be a "Jewish Terrorist" or a "Muslim Terrorist." Some people like to claim that the Israeli Army is a terrorist organization because that hyperbole is useful in poisoning the well in any discussion about Israel, even though the Israeli Army does not qualify under the traditional qualifications of terrorism as popularly understood.

JEWISH TERRORISM
The "typical" Jewish terrorist organization is the Irgun which was a group led by Menachem Begin the British Mandate of Palestine and Israel from the 1930s-1949 before being absorbed into the Israeli Defense Forces and changing its tactics to more acceptable forms of warfare. The Irgun operated similarly to the IRA, planting bombs in cars or in offices near to prime political targets. The other major Jewish organization was the Lehi which operated in roughly the same time period and was responsible for political assassinations and fear incitement. The assassination of Swedish diplomat Bernadotte led to the Israeli Prime Minister Ben Gurion ordering the immediate disbanding of Lehi and the criminalization of its membership. The Irgun and Lehi were also notable for the Rape of Deir Yassin which was the bloodiest act in the Jewish-Arab Engagement of 1947-1949.

ISLAMIC TERRORISM
There are a wide variety of Muslim terrorist organizations, but most have certain discernible characteristics. The most common and identifiable Muslim terrorist action is the suicide bomber who blows himself up to take out some enemies as well as himself. Muslim terrorist organizations tell their membership that the fight in which they are engaged is part of the holy Islamic struggle of Jihad and anyone who opposes them is not properly guided. Therefore, Muslim terrorist organizations will identify what sect of Islam they belong to and whether or not they oppose the other sects. Most Muslim terrorists wish to inspire fear in their enemies and therefore primarily attack civilians, considering them part of the enemy. Some "moderate" non-associated clerics have defended these activities claiming that the civilians represent part of the group that "is opposed to Islam". Since Muslim terrorists exist in countries with a weak internal support structure, in many cases such as with Hezbollah, Hamas, or Fatah, they will use their own funds to build schools, parks, hospitals, and other social services in the communities they occupy. It provides goodwill with the local inhabitants and allows them to more effectively spread whatever messages they may wish to say. Finally, Muslim terrorist organizations like Hezbollah, Hamas, and Fatah have all actively engaged in elections (Hezbollah in Lebanon, Hamas and Fatah in Palestine) with their own political parties. If the governments formed after these elections were not desirable to these parties, they engaged in military actions to force the national government to capitulate to their desires. In the case of Hezbollah this created a violent stand-off in Beirut and in the case of Hamas and Fatah, this prompted a Palestinian Civil War in Gaza and the West Bank.

So, in summation there are several notable differences:

Religion: While Jewish terrorists are ethnically Jewish, they are motivated by exclusively political causes, Muslim terrorists are motivated for religious and political causes.
Targeting: While Jewish terrorists usually go after military and political targets, Muslim terrorists usually go after a civilian population.
Methods of Attack: While Jewish terrorists typically use guns (for assassinations) or car-bombs, Muslim terrorists use suicide bombers, rockets, missiles, and, in some cases, military vehicles.
Non-Military Wings: While Jewish terrorist organizations solely deal with militant activities, a number of Muslim terrorist organizations provide healthcare, schooling, and social services to the nearby Muslim community and run political parties in addition to their military activities.
Governmental Assumption: While Jewish terrorists have never attempted to gain direct power though either a coup d'Ã©tat, military pressure, or elections, several Muslim terrorist organizations have assumed power through just such actions.

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