* Kosovo votes under shadow of war crimes investigation
* Thaci bidding for third term as prime minister
* Voters angry over poverty, corruption (Adds turnout, quotes)
By Fatos Bytyci and Matt Robinson
PRISTINA, June 8 (Reuters) - Kosovo voted in an election on Sunday marked by voter frustration over poverty and corruption six years after seceding from Serbia, testing ex-guerrilla Hashim Thaci's bid for a third term as prime minister.
Some analysts expect the closest race since 46-year-old Thaci presided over Kosovo's Western-backed declaration of independence in 2008.
If he wins, Thaci will come under immediate pressure from the West to heed the findings of a war crimes investigation that threatens to ensnare his former comrades-in-arms.
Frustration with Kosovo's progress is running high among many of its 1.8 million people, who rank among Europe's poorest. A third of the workforce is unemployed. Corruption is rife.
Five hours after polls opened, only 14 percent of eligible voters had cast their ballots. Voting appeared to be slow among ethnic Serbs in a pocket of northern Kosovo that the European Union is trying to integrate in agreement with Serbia.
"This old class of politician has been around for 15 years and had plenty of time to profit," said Muhamet Maqastena, a trader in the capital, Pristina. "It's time for them to go and let the young, educated people govern us."
Valbona Bajraktari, a 37-year-old unemployed woman, said her expectations were not high. "The only thing I want is for them not to steal or to hire their aunts," she told Reuters.
Fighting back, Thaci's government raised public sector wages, pensions and social welfare benefits two months ago by 25 percent. That directly affects 240,000 teachers, doctors, police officers, pensioners and others, and even more indirectly.
He has promised to do the same every year if given a new four-year mandate.
"Our state is a new European state, a state that has great opportunities, and I'm committed to making the most of them," Thaci said after voting in a Pristina school.
The next government, however, will face a challenge within weeks when a special European Union task force is expected to issue the findings of an investigation into allegations that Kosovo's guerrilla army harvested organs from Serb prisoners of war and sold them on the black market during a 1998-99 conflict.
The investigation followed a 2011 report by Council of Europe rapporteur Dick Marty which pointed the finger at Thaci and other ex-rebels, including four senior members of the prime minister's Democratic Party of Kosovo (PDK) and candidates for parliament.
Thaci has dismissed the allegations as an outrage, a bid to tarnish the Kosovo Albanian fight for freedom that eventually won NATO air support.
The West wants a court set up abroad to hear the case because of witness intimidation in Kosovo and a graft-riddled legal system. That will require changes to the law and constitution.
Thaci was one of the leaders of the Kosovo Liberation Army that took up arms in the late 1990s to break free from the repressive rule of Serbia under strongman Slobodan Milosevic.
NATO intervened in 1999 with 78 days of air strikes against Serbia, trying to halt the massacre and mass expulsion of Kosovo Albanians by Serbian forces waging a counter-insurgency.
Kosovo declared independence almost a decade later and has been recognised by more than 100 countries, but not Serbia or its big-power backer Russia, which is blocking the young state's accession to the United Nations.
Its economy is forecast to grow by at least 3 percent this year, driven by construction and cash sent home by Albanians working abroad. Even that, however, is not enough to absorb the thousands of jobseekers entering the workforce every year in what is Europe's youngest society.
Opinion polls are not reliable, but they suggest that the PDK has a slight lead over the LDK, the Alliance for the Future of Kosovo (AAK) and the leftist Self-Determination party.
Haki Jashanica, a 56-year-old former teacher, said of Thaci's PDK: "If this party continues in the same vein, in terms of the economy and raising salaries, then it will be a pleasure to have them in power again."
Polls close at 7 p.m. (1700 GMT). Preliminary official results are expected by midnight (2200 GMT). (Editing by David Goodman)