Former Kosovo health minister Ilir Rrecaj -- who admitted during the trial that he knew that illegal kidney transplants were carried out at the Medicus clinic in Pristina in 2008, but denied covering them up -- was acquitted.
Prominent Pristina urologist Lutfi Dervishi got the stiffest term of eight years for "organised crime and human trafficking," the judge said in the verdict.
His son Arban Dervishi was sentenced to seven years and three months while the other three defendants received between one and three years imprisonment.
The indictment says that at least 30 illegal kidney removals and transplants were carried out at the clinic in the Kosovo capital in 2008.
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Police raided the clinic after a Turkish man collapsed at Pristina airport waiting for a flight back to Istanbul after having had a kidney removed.
The donors were recruited from poor Eastern European and Central Asian countries who were promised about 15,000 euros for their organs, while recipients would pay up to 100,000 euros each.
The recipients were mainly Israelis.
The indictment names Israeli national Moshe Harel as the mastermind of a network for recruiting donors and finding recipients, while Turkish doctor Yusuf Sonmez is said to have performed organ removal surgery at the clinic.
But the two were not among those on trial in Pristina as they were not available to the court.
The case is being tried by EULEX, the European rule of law mission in Kosovo, set up to help the local judiciary handle sensitive cases after the territory declared independence from Serbia in 2008.
Prosecutor Johnathan Ratel had requested testimony from Dick Marty, the Council of Europe's rapporteur on alleged organ trafficking during the 1998-99 Kosovo war.
But the request was rejected by the procedural board of the Council of Europe's Parliamentary Assembly.
Marty had alleged that senior commanders of the ethnic Albanian guerrilla Kosovo Liberation Army (KLA), including current prime minister Hashim Thaci, had been involved in organised crime and organ trafficking during and after the war.
The report set out claims that organs were taken from prisoners, many of them Serbs, held by the independence-seeking KLA rebels in Albania in the late 1990s.
Both Kosovo and Albania denied the accusations and rejected the report.