In 1999, the United States and NATO fought a war against “ethnic cleansing” in Kosovo by forces of the Federal Republic of Yugoslavia. On the ground, a guerrilla group of Kosovar Albanians called the Kosovo Liberation Army (KLA) allied with the United States and NATO in the war against the Yugoslav forces, led by Slobodan Milosevic. International support for the KLA in the nearly three-month campaign was strong. The war became cast as a battle for human rights and international order. At the end of the fighting, on June 10, 1999, then-U.S. President Bill Clinton, winding up a presidency tainted by American passivity during the slaughters in Bosnia and Rwanda, proudly proclaimed: “Because of our resolve, the 20th century is ending, not with helpless indignation, but with a hopeful affirmation of human dignity and human rights for the 21st century. For in Kosovo we did the right thing. We did it the right way. And we will finish the job.” Twelve years later, few would argue that the war was not justified. But the U.S.-backed KLA leaders who went on to be elected to run Kosovo are now being investigated for operating what amounts to an organized crime syndicate with allegations of murder as well as widespread trafficking of women, narcotics and even human organs. And, as a GlobalPost investigation has found, American and NATO officials had evidence of the criminal allegations all along.

PRISTINA, Kosovo — It was the fall of 2000, just over a year after the end of the war in Kosovo, when two NATO military intelligence officers produced the first known report on local organized crime, painting the former political leader of the Kosovo Liberation Army (KLA), Hashim Thaci, as having “established influence on local criminal organizations, which control [a] large part of Kosovo.”

The report, the existence of which has not been previously reported, was widely distributed among all NATO countries, according to former NATO sources interviewed by GlobalPost. And year after year as the nascent democracy of Kosovo struggled to move forward and Thaci rose to political prominence, more detailed allegations and intelligence reports, totaling at least four more between 2000 and 2009, would name Thaci, these sources add. The reports were widely available to U.S. and NATO intelligence officials, and at least two were readily available on the internet. In one 36-page NATO intelligence report obtained by GlobalPost, Thaci merits a page to himself with a diagram linking him to other prominent former KLA members who are themselves linked to various criminal activities that include, extortion, murder and trafficking in drugs, stolen cars, cigarettes, weapons and women.

A diagram from a NATO intelligence report detailing alleged links between the current prime minister of Kosovo, Hashim Thaci, and other people alleged to be involved in organized crime in Kosovo.

Today, Thaci is the prime minister of Kosovo. In fact, he was just recently re-elected to his second term.

In spite of U.S. officials knowing about the numerous and detailed allegations against Thaci and many of his former colleagues in the KLA, he has remained a valued ally of successive U.S. administrations. It is unknown which U.S. officials have seen the reports. But a NATO diplomat said it was common knowledge that Thaci is suspected of criminal activity: “Whenever you looked at him always in the briefings it was ‘suspected of organized crime.’”

And when asked if he heard the accusations against Thaci and others over the years, Daniel Serwer, a former senior American diplomat in the Balkans and now a senior fellow at the Center for Transatlantic Relations at the Johns Hopkins School of Advanced International Studies, said, “Absolutely. It’s been a common allegation.”

Former Secretary of State Madeleine Albright publicly embraced Thaci. Former President George W. Bush hosted him in the Oval Office. Vice President Joseph Biden also welcomed him to the White House, in July. Secretary of State Hillary Clinton visited him in Kosovo as recently as the fall.

“I want you to know, prime minister,” Clinton said to Thaci, during her visit to Pristina on Oct. 13 last year, “that just as we have been with you on the hard road to independence, we will stay with you. We are your partners and we are your friends and we are very committed to your future.”

Serwer said that Clinton has “certainly heard the allegations against them … . We all heard them.”

Kosovo, a fledgling democracy that the United States and NATO together helped liberate and then create in a globally popular war that was partly framed by the United States and its allies as a war of humanitarian intervention, is now hamstrung by corruption and intimidation.Thaci and many of his fellow Kosovo Albanian guerrilla leaders who were key U.S. and NATO allies in the 1999 war have clung to power and are facing numerous allegations of criminal wrongdoing. In a country whose very existence was fuelled by the West’s concern for human rights, many citizens are afraid to criticize a prime minister and his allies, who stand accused of routinely violating human rights.

Based on three months of reporting, involving dozens of interviews with politicians, former KLA members, diplomats, former NATO soldiers, political analysts and officials, GlobalPost has found that concerns about criminality among Kosovo’s ruling political class went largely ignored by the United States, NATO and the United Nations over the past 11 years — and in some cases U.S. and U.N. officials thwarted criminal investigations into former senior KLA figures. That, according to many of these people who have played a part in Kosovo’s recent history, was because the United States, NATO and the United Nations believed that keeping the peace in Kosovo between its ethnic majority Albanians and minority Serbian population — and Serbia itself — was a priority that outstripped all other concerns, including allegations of horrific human rights abuses.

At the same time, the KLA were cast as Kosovo’s heroes and its leaders emerged from the war with unparalleled political popularity and power, which limited the options of the United States and other NATO countries in finding effective partners in Kosovo. “It’s very easy to be holier than thou but in the end in places like this you’re going to meet people who are not good,” the NATO diplomat said. “If they were good people then probably they wouldn’t be in power or you wouldn’t have a problem with the country in the first place. It’s the price of doing business.”

Thaci has not been charged in a criminal case, but the timeline of the mounting allegations against him reveal that U.S. and NATO officials knowingly supported him and other Kosovo leaders who were purportedly involved in serious crimes right from the start of the Kosovo conflict.

“Americans and those who were in charge had access to this and other documents,” said a Western diplomat with knowledge of the region, referring to the intelligence report that is marked on every page as being for the viewing of the United States and NATO. Four other diplomatic, military and intelligence sources confirmed the documents were seen by U.S. officials.

Referring to the 2000 report, a former NATO intelligence officer in Kosovo who had access to a wide array of information relating to organized crime said that the United States and other NATO countries “did nothing after its publication, which made me disappointed and disheartened.”

Florin Krasniqi, a Brooklyn-based businessman who raised large amounts of money for the KLA and shipped high-powered rifles from the United States to the KLA, said he has personally complained to senior State Department officials about corruption and crime at the top levels of government in Kosovo but he said he is routinely dismissed.

“You can be corrupted as hell,” Krasniqi said, “but as long as you keep the stability you are a friend.”

Krasniqi, who was recently elected to the Kosovo parliament, described his former KLA comrade Thaci as “the head of the mafia here.”

Thaci is a telegenic, commanding figure who speaks passable English. He first became close to American officials during peace negotiations in France in March 1999, prior to the outbreak of war.

“I don’t think there’s any escaping the fact that these allegations have been around for a long time and in order to put them to rest there has to be a serious investigation,” said Serwer. Thaci, whom Serwer knows, “would like it to just go away. But I don’t see how it can go away.”

Some of the longstanding suspicions about Thaci and his associates were brought into stark and public focus in December when a Swiss senator named Dick Marty published a report under the auspices of the Council of Europe, a respected human rights organization, accusing Thaci and other prominent former KLA commanders of being involved in numerous crimes, including trafficking in human organs harvested from people who were allegedly killed for that purpose.

Then-State Department spokesman P.J. Crowley responded to the release of the report in December, saying that “any evidence and sources cited in this report should be shared with competent authorities to conduct a full and proper investigation.”

But beyond that, administration officials are reluctant to discuss why successive American governments have backed Thaci even though every administration since Bill Clinton’s has had access to the detailed allegations of Thaci’s alleged ties to organized crime.

The U.S. ambassador to Kosovo, Christopher Dell, declined numerous requests for an interview. A spokeswoman agreed to accept questions for a possible response from Dell, but then he declined to answer any. State Department officials, including former ambassador and current Deputy Assistant Secretary of State Tina Kaidanow, also declined to comment. Other officials and former officials declined to comment, including Secretary of State Clinton, former Secretary of State Albright and Albright’s former spokesman Jamie Rubin.

A spokesman for Thaci also declined numerous requests for an interview, saying that Thaci was too busy. Thaci also did not respond to written questions. Thaci is threatening to sue Marty over the report. Thaci has called the report “scandalous” and has said that its aim was “to devalue both the KLA and the independence of Kosovo.”

Criminal investigations

Beyond intelligence reports and mounting allegations, several criminal investigations of Thaci’s allies were known to U.S. officials — and three are a matter of public record.

GlobalPost has obtained a case report from the now-defunct U.N. mission in Kosovo’s War Crimes Unit, dated May 20, 2008. The case report describes how, shortly after the war, German NATO soldiers found and released 14 people who were being illegally detained by the KLA in the city of Prizren in southern Kosovo. They also found the body of an elderly Kosovo Albanian man who was still handcuffed. He “showed signs of having been beaten,” the reports reads.

Among those named as suspects in the report is Kadri Veseli, who is considered by many in Kosovo to be Thaci’s closest ally. Veseli was chief of SHIK, the KLA’s intelligence service, an organization that continued to exist and operate without legal sanction until 2008, and possibly exists to this day. In addition to Veseli, other senior KLA commanders and Thaci allies, including Azem Syla, Sabit Geci and Fatmir Limaj, are also named as suspects in the report.

None have ever been charged in relation to the alleged crime in Prizren. But Syla, Geci and Limaj have also been subject to other criminal investigations.

Syla was arrested by police in late 2009 and questioned about whether he was involved in ordering SHIK hitmen to kill a political opponent. Syla has not been charged in the case, whose star defendant is likely to be a self-professed SHIK assassin named Nazim Bllaca.

Limaj, another senior former KLA leader and Thaci’s former minister of transporation, was charged with war crimes in mid-March by EULEX, a mission of the European Union that works with Kosovo officials on enforcing the rule of law.

Last year EULEX investigators raided and searched Limaj’s homes and places of work. He has not been indicted but many observers in Kosovo believe he is, or was, under investigation for massive corruption related to road construction contracts as well as war crimes. (Limaj was acquitted of war crimes by the International Criminal Tribunal for the former Yugoslavia.)

Geci is currently on trial, charged with war crimes by EULEX prosecutors. The EULEX investigation into Geci features Thaci in a cameo, GlobalPost has learned. Prosecutors and witnesses allege the during the war Geci ran a prison in the KLA headquarters in the town of Kukes. In the prison, prosecutors and witnesses say, Geci tortured numerous Albanian prisoners suspected of being collaborators or political opponents of the KLA.

In an interview, one of the estimated 20 survivors of the prison said that he saw Thaci present at the prison. The man, who says Geci tortured him and murdered his brother, has agreed to testify in Geci’s trial but requested anonymity before agreeing to an interview.

“I saw Hashim Thaci with my own eyes,” said the man, acknowledging that it was possible that Thaci did not know the prisoners were being tortured at the KLA base. But, the man said, the prisoners were held in a room with a large window and “he could see us.”

The man said he has told EULEX prosecutors about seeing Thaci at the prison camp. EULEX prosecutors declined to discuss the case.

If a reckoning of some senior KLA leaders is perhaps beginning with Geci’s trial, it has been too long in coming, critics say. Among those critics are people whose job it was to investigate and prosecute criminals in Kosovo after the war.

Protected by the United States?

One of the most frustrating examples of American power in the capital Pristina, say current and former U.N. officials and Western diplomats, was the influence American diplomats exerted over the supposedly independent U.N. prosecutor’s office in Kosovo.

“There was interference by the U.S. mission [to Kosovo] preventing effective investigation and prosecution of senior Kosovo officials,” said a U.N. official, who is in a position to know about the details of the United Nations' law enforcement efforts during the time that it administered Kosovo, from 2000 to 2008.

The official said that the senior Kosovo politicians were being investigated for being allegedly involved in organized crime, and that U.S. officials prevented searches of the suspects’ homes and in one case were involved with U.N. officials in preventing a sentence from being carried out. The U.N. official said that these phone calls were “well known” and deeply frustrated many of the international prosecutors who were working for the United Nations and wanted to prosecute these Kosovo officials.

On June 14, 2008, the most senior U.N. official in Kosovo, Joachim Ruecker, issued an executive decision suspending the prison term of a former KLA commander named Sami Lushtaku, who had been sentenced to a total of 11 months in prison. Lushtaku was mayor of a town named Skenderaj, where support for the KLA is strong. In his order, which GlobalPost has obtained, Ruecker notes that Lushtaku’s sentence would make him legally ineligible to be mayor and “such an outcome would be politically highly sensitive at this stage and contrary to the public interest.” It is unknown if American officials influenced Ruecker’s legal decision, but a former senior NATO official in Kosovo said that CIA officials in Kosovo had tried to prevent NATO soldiers from arresting Lushtaku prior to prosecution.

Other officials and former officials confirmed that the United States protected some senior political figures, including former KLA leaders close to Thaci, for the sake of creating the impression that Kosovo was a stable country with strong local leaders. The same officials and former officials said that other NATO and U.N. officials were often complicit in suppressing investigations, although many others were angry at the blocked investigations.

“When we talked to them [the former KLA commanders who are still very influential in Kosovo today] we all knew they lied to us and they knew that we knew they were lying but there was not much we could do thanks to politics and their patrons in D.C.,” a former NATO intelligence official who worked in Kosovo told GlobalPost. “They freely run prostitution, petrol smuggling, money laundering, racketeering, intimidation of LDK people [members of a rival political party, the Democratic League of Kosovo]. They get away with murder.

“The Americans were not making criminal investigations easy,” the former NATO intelligence official said. “In a couple of cases that I know of they wanted investigations to freeze because that ‘was not the right time to do it,’ according to them, so they just pulled the plug and there was nothing that we could do. It concerned the big fish.”

A former international monitor with connections to the U.N.’s mission in Kosovo said: “It got to the point where some of my prosecutor friends were told not to do this. One can understand if someone says wait. They might be told hold for a while. But for people to just flat out say ‘don’t you do this ever’ and to treat the prosecutor’s office as an extension of the political office — that’s where lines get blurred.”

The former monitor sat in on meetings involving U.S. diplomats in which they and U.N. officials discussed whether political considerations should prevent certain political figures from being investigated or arrested.

The sense that Thaci and his close associates are protected and untouchable has created what many observers in Kosovo describe as a sense of hopelessness. Thaci is building a large house in the capital, Pristina, and even if the money for the construction comes from legitimate sources many ordinary Kosovars, who are the poorest people in Europe, see the house as a symbol of arrogance and corruption.

“To me this is absolutely reprehensible,” Serwer said.

It is highly unlikely that Thaci would ever be prosecuted by a Kosovo court. “The police, public prosecutors and courts are erratic performers, prone to political interference and abuse of office,” the non-partisan International Crisis Group wrote in a report last year, echoing a view shared by many Kosovars, foreign governments and aid groups.

A GlobalPost reporter interviewed Kosovo’s chief of police, Reshat Maliqi, and asked him why he had not initiated an investigation into Thaci or ordered his officers to search for evidence, given the numerous allegations against the prime minister. “We didn’t try,” Maliqi said, “because someone needs to knock on my door” bringing evidence.

If anyone is to prosecute Thaci it would almost certainly have to be international prosecutors. Since 2008 EULEX has been the most powerful judicial force in Kosovo, which declared independence the same year. Thaci’s opponents and critics hope that EULEX prosecutors will aggressively investigate the prime minister.

A Western diplomat based in Kosovo confirmed to GlobalPost that EULEX had been quietly investigating Thaci for some time. And in January EULEX announced its prosecutors had opened a preleminary investigation into the organ-trafficking allegations in Marty’s report.

There are signs that Thaci’s friends in Washington are becoming increasingly embarrassed by the swirl of corruption and crime that surrounds him and other former KLA commanders.

When Thaci visited Biden in July, Biden was all smiles in public with Thaci but “hammered” him about corruption in their private meeting, according to someone with knowledge of the meeting. Thaci agreed with Biden that there was a problem and said he would try harder to stop corruption and crime in the Kosovo government.

And if Thaci wants to visit the United States again it is now unlikely that he would ever be able to obtain a U.S. visa other than a diplomatic visa, which grants him immunity, U.S. government sources told GlobalPost. The United States does not generally allow foreign nationals into the country when there are unresolved allegations of human rights abuses against them. Thaci has told associates that he is now concerned about traveling overseas because he fears being arrested in a foreign country.

Thaci remains by far the most powerful politician in Kosovo. But if the United States were to withdraw support for him, or for his country, Kosovo would be plunged into political chaos that some people believe would lead to the break-up of the country. Such chaos also comes with a danger of resumed ethnic hostilities.

“At one point the United States is going to say you don’t deserve a country,” said Engjellushe Morina, executive director of the Kosovo Stability Initiative think-tank in Pristina. “Some of Kosovo will go to Albania and some will go to Serbia. It would be a disaster for that to happen. We so badly wanted a state and we didn’t know how to run a state.”

Jovo Martinovic contributed to this story.

Matt McAllester, a Pulitzer Prize-winning reporter and long-time foreign correspondent, is a regular contributor to GlobalPost's "Special Reports." McAllester and Jovo Martinovic have both been reporting on war crimes and organized crime in the Balkans for over a decade. Their work includes investigations of Serbian war crimes during the wars in Bosnia and Kosovo and the GlobalPost exclusive on the Pink Panther jewelry thieves.

(GlobalPost funding for human rights reporting on stories like these is provided in part by a grant from the Galloway Family Foundation.)