SLATINA, Kosovo, April 4 (Reuters) - Thousands of flag-waving Kosovo Albanians turned out on Friday to welcome home ex-prime minister Ramush Haradinaj after his acquittal at the U.N. war crimes tribunal in The Hague.

The former guerrilla commander, who fought Serb forces in 1998-99, returned to Kosovo six weeks after the territory declared independence from Serbia and won recognition from major Western powers. "I am here, where I belong, with the people of Kosovo. And I feel great," the 39-year-old told several thousand people at Slatina airport as they chanted his name and threw flowers.

"The Kosovo Liberation Army fought a just war," he said.

Haradinaj, the most senior Kosovo Albanian to be tried by the U.N. tribunal, was cleared on Thursday of persecuting Serbs during the two-year guerrilla war for independence.

The ruling compounded Serb anger over Kosovo's secession and revived accusations by Belgrade that the court is anti-Serb.

Analysts said the verdict played into the hands of nationalists ahead of Serbia's close parliamentary election on May 11, and might make it harder for any Serb government to justify handing over four remaining Serb war crimes fugitives.

Nationalist Serbian Prime Minister Vojislav Kostunica said the ruling made a "mockery of justice".

"Every citizen of Serbia knows that with this decision the Hague tribunal has rewarded crime and humiliated innocent Serbian victims," he said on Friday.

He called on the European Union to review whether Serbia's further integration with the bloc should depend on its cooperation with the tribunal, as has been the case until now.

Haradinaj, a former nightclub bouncer, was prime minister for a few months until he resigned in 2005 after being indicted. He is expected to return to politics as head of the small party Alliance for the Future of Kosovo.

Considered a hero by many Kosovo Albanians, Haradinaj was acquitted of torture, murder, rape and deportation after the Kosovo Liberation Army launched a guerrilla war to end a decade of Serb repression under late strongman Slobodan Milosevic.

Serb forces expelled almost one million Albanians.

Judges said the prosecution had failed to prove a deliberate campaign to kill and expel Serb civilians from Kosovo. They also noted prosecution complaints of witness intimidation throughout the trial.

Haradinaj's uncle, Lahi Brahimaj, a senior KLA figure, was cleared of most charges but sentenced to six years jail for personally taking part in the cruel treatment of a detainee at a camp, and ordering the mistreatment of a perceived collaborator.

A third accused, Idriz Balaj, the commander of the KLA's "Black Eagles" special unit, was cleared of all charges of torture, murder, rape and deportation. (Writing by Matt Robinson; editing by Tim Pearce)