A Serb paramilitary commander during the Balkan wars of the 1990s has pleaded not guilty at the start of his war crimes trial in Croatia.

Dragan Vasiljevic, also known as Captain Dragan and Daniel Snedden, is charged with killings and torture of civilians while he was a rebel Serb commander during the 1991-95 Croatian war.

The charges carry a maximum 20-year prison sentence in Croatia.

Vasiljkovic, who was born in Serbia, went to Australia at the age of 15 but returned to the Balkans to train Croatian Serb rebels in 1991, when Serbs took up arms against Croatia's secession from Yugoslavia.

He has been in custody since he was extradited from Australia in July last year after fighting a 10-year legal battle against being handed over to the Croatian judiciary.