AMSTERDAM, March 17 (Reuters) - Two former top Serbian security officials go on trial at the U.N. war crimes tribunal on Monday charged with having run secret militia units that murdered and persecuted non-Serbs during the Balkan wars. Jovica Stanisic, the late Serbian President Slobodan Milosevic's secret service chief, and Franko Simatovic, a commander of elite Serb forces, face charges including murder and deportation for arming and training units which acted in tandem with other Serb forces fighting in Croatia and Bosnia. Prosecutors say the two participated in a larger project, alongside Milosevic and others, to ethnically cleanse swathes of Bosnia and Croatia by permanently removing Croats, Muslims and Bosnian Croats from those areas between 1991 and 1995.

The two accused, both aged 57, have pleaded not guilty.

Charges relate to the actions of some of the most notorious militias of the Balkan wars including the Scorpions and Arkan's Tigers, and the indictment lists hundreds of execution-style murders.

U.N. prosecutors first indicted the pair in May 2003 and Serb authorities transferred them to The Hague that year. They were later granted provisional release pending the start of their trial. (Reporting by Alexandra Hudson, editing by Tim Pearce)

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