Yusuf Sonmez, 53, is among at least nine people who were indicted in the case in Kosovo, which declared independence in 2008 and has struggled to shake off organized crime and corruption under international supervision.
Interpol had issued a notice requesting the arrest of Sonmez over the Kosovo case, though he has been detained in Turkey in the past. A warrant issued by the district court in Pristina, the capital of Kosovo, charges him with people smuggling and illegal immigration.
Kristiina Herodes, spokeswoman for European Union police in Kosovo, welcomed Sonmez's arrest and said it was carried out based on the Pristina warrant. She said it was too early to comment on whether he would be extradited.
Herodes said the EU prosecutor in charge of the case, Jonathan Ratel, was working closely with Turkish judicial authorities on parallel investigations in Kosovo and Turkey.
Ratel said in his indictment that an alleged gang enticed people into Kosovo to remove their organs. At a hearing last week, he said poor people were given false promises of payment for their kidneys, which were then sold to organ recipients in illegal transplants.
Ratel described Sonmez as a "key surgical participant" in operations performed in a private clinic on the outskirts of Pristina.
The judge has less than two weeks to decide if the case will move to a trial. Kosovo's justice authorities are monitored by an EU mission that also deals with serious crimes.
Sonmez has previously been arrested in Turkey on suspicion of illegally procuring kidneys from destitute Turks and transplanting them to patients for large profits, according to Turkish media. Most organ recipients were from other countries.
Sonmez dodged any extensive prison term by producing documents from donors attesting that no money was ever exchanged, Vatan newspaper quoted Ilhan Dogan, a former health ministry inspector, as saying. Because organ donation is low, Turkey's laws allow people who are not blood relatives to donate their kidneys to needy patients as long as no money changes hands.
Doctors have to refuse transplants if they suspect any transaction.
In statements posted on his website, Sonmez said he has also worked at a clinic in Baku, Azerbaijan. He claimed he was unfairly hounded by the Turkish media, and denied any wrongdoing in the Kosovo case.
"I am being shown as the biggest criminal and even the leader of a criminal gang," he wrote. "If I am the gang leader, where are my men?"