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The U.N. war crimes tribunal in The Hague on Thursday acquitted a former commander of the rebel Kosovo Liberation Army of all charges of war crimes in a decision that could inflame anti-Kosovo sentiment in Serbia just weeks after Kosovo unilaterally declared independence.

The commander, Ramush Haradinaj, who also briefly served as prime minister of Kosovo three years ago, was found not guilty of murder, persecution, rape and torture of Kosovo Serb civilians and some ethnic Albanians. The crimes were said to have been carried out by men under his command in 1998, when the rebels fought to free their largely ethnic Albanian region from Serbian rule.

Another rebel commander, Idriz Balaj, was also acquitted, while a third defendant, Lahi Brahimaj, was sentenced to six years in prison for torture and cruel treatment of prisoners.

The two men who were acquitted, who may return home as early as Friday, are expected to be given heroes’ welcome. But in summarizing their verdict, the judges said that the trial had been subject to many shortcomings, including vague evidence and widespread fear among witnesses, suggesting that the full version of events had not been told.

The full judgment is not yet available, but in their summary, the judges gave much weight to the fear and the evident intimidation of witnesses. They stressed that the court, though it heard almost 100 witnesses, had serious difficulties in getting many of them to testify freely. They said that they had to grant 34 witnesses permission to hide their identities from the public, that 18 were subpoenaed because they refused to testify and that others said they dared not talk once they were in court.

The case against Haradinaj was fraught with difficulties from the start. Western diplomats tried to dissuade Carla Del Ponte, who was chief prosecutor, from an indictment of Haradinaj, arguing that he was a respected political leader who played a necessary and important role in stabilizing Kosovo.

Within the prosecutor’s office, some lawyers also warned from the start that the case against Haradinaj was weak because it would be difficult to link him to the crimes.

Prosecutors complained repeatedly about pressure on the witnesses, saying that it had been greater than in any other trial at the tribunal.

Those most afraid, prosecutors said, were former fellow rebel fighters who had been expected to testify as insiders. At least three designated witnesses were killed before the trial, prosecutors said.

Last November, the trial ground to a halt when the defense lawyers for all three accused unexpectedly announced they would not call any witnesses of their own because they considered the prosecution case so weak.

For Serbs, the acquittal of two of the former rebel commanders, whose forces were backed and supported by the West, is likely to be viewed as one more insult.

Kosovo has long been portrayed as a victim of Serbia. Only one other case at the tribunal has focused on the abuses and killings by fighters of the Kosovo Liberation Army, although human rights groups have documented numerous killings and instances of mistreatment of those not siding with the rebels.