Naser Oric was accused of killing three Serb prisoners of war in villages around Srebrenica in the early days of the conflict.
A panel of judges ruled Friday that the prosecution didn't present evidence proving the case against Oric.
This was the second time that Oric was acquitted in a trial which opened in January 2016.
Oric had also been tried by a UN war crimes tribunal where he was also acquitted in 2008. (AP)
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