Witness Abdullah Mohammed Hussain said he met Saddam in 1989 after he returned from Iran, where he had fled to escape the brutal Anfal campaign which prosecutors claim killed 182,000 Kurds.
Taking the witness box, Hussain described the 1988 attacks on his northern village near Sulaimaniyah and recounted his meeting with Saddam, which he said had materialised after repeated requests to the Iraqi military.
"I told Saddam they (relatives) were arrested in our village," Hussain said.
"Saddam said ... 'Shut up. Don't say that they went missing in Anfal,'" Hussain said as the former military strongman watched from the dock.
He was later told in 2004 by the Sulaimaniyah court that the ID cards of his relatives were found in a mass grave in Hathat, near the northern city of Mosul.
Hussain was the 18th witness to testify against the accused since the trial began on August 21.
Saddam and six others are in the dock facing charges over the former regime forces' bombing, imprisonment, killing and burial of Kurds in mass graves during the Anfal attacks that coincided with the last years of the 1980-1988 Iran-Iraq war.
If found guilty the defendants will face execution by hanging.