Col. Dragan Obrenovic also is accused of trying to cover up the largest massacre in Europe since World War II by exhuming the bodies of victims and reburying them in mass graves.
Obrenovic, 38, made his first appearance before the U.N. war crimes tribunal for the former Yugoslavia since his arrest Sunday in Zvornik, Bosnia, by NATO-led peacekeeping forces.
He could face a maximum sentence of life imprisonment if found guilty of one of five counts of complicity in genocide and crimes against humanity for the extermination, murder and pmrSacution of Muslims.
"Your honor, I am not guilty," Obrenovic told the presiding Australian judge, David Hunt.
Dressed in a black suit, crisp white shirt and tie, Obrenovic stood nervously with his hands clasped before him as he entered a separate plea to each of the five charges.
According to the indictment, Obrenovic was the acting commander of the Zvornik Brigade, which rounded up victims in 50-60 buses and took them to execution sites, including schools, soccer fields, a cultural center and a dam.
Eyewitnesses said the bodies of the executed were transported in truckloads to common graves. Some were dug up later and relocated to try to keep the killings secret.
The court already has been hearing testimony about the Srebrenica massacre from witnesses in the trial of Gen. Radislav Krstic, Obenovic's commander.
Last year, the prosecution played a recorded radio intercept of a conversation allegedly between Krstic and Obrenovic about the hunting down of survivors. The poor quality recording was dated Aug. 2, 1995. Krstic denied the recording was authentic.
"Krstic here," the first voice says. Are you doing your job down there?"
"Of course we're working," answers a second voice, allegedly that of Obrenovic. "We've managed to catch a few more, either by gunpoint or in mines."
"Yes, kill every single one of them," the first voice says.
"Everything is going according to plan," the second says.
"Not a single one must be left alive," the first voice responds.
The United Nations had designated Srebrenica a "safe haven," where militants were to be barred and civilians protected, and posted 150 Dutch troops there to protect the town of 60,000 residents in eastern Bosnia.
But Serb forces, who alleged that Muslim militants were using the safe haven as cover, easily overran the town. The United Nations in 1999 acknowledged its error in expecting 150 Dutch troops to deter thousands of Serb fighters.
Also under indictment for Srebrenica are two of the most wanted fugitives of the 1992-95 Bosnian war, wartime Bosnian Serb leader Radovan Karadzic and his top general, Ratko Mladic.
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