"Not guilty," Djordjevic said in response to five charges of forcible transfers, deportations, murders and expulsions of 800,000 Kosovo Albanians in the first half of 1999.
He served as assistant minister of the interior and chief of the public security department at the time.
Djordjevic was arrested last month in Montenegro where he had been hiding under an assumed name since early 2003. He left Serbia in 2001 and hid in several countries before arriving in Montenegro.
Djordjevic said that the Montenegrin authorities had not known that he had been hiding there. Media previously speculated that was hiding in Russia.
Djordjevic was indicted in late 2003.