Critics say the present government is punishing him for refusing to testify his former president.
"The Iraqi government also wants to avoid the public criticism for keeping an ailing man in prison for five years without presenting any charges against him," Aziz's son, Ziad, said in a telephone interview from Jordan.
The merchants were rounded up over two days in July 1992 from Baghdad's wholesale markets and charged with manipulating food supplies to drive up prices at a time when many Iraqis were suffering economically.
All 42 were executed hours later after a quick trial.
Aziz's co-defendants include Saddam's half brother, Watban Ibrahim al-Hassan, and cousin Ali Hassan al-Majid, also known as "Chemical Ali", who has been sentenced to death in another case.
A judge with the Iraqi High Tribunal, who declined to be identified, said the charges against the defendants would include war crimes, crimes against humanity and genocide.
If convicted, the men could face death by hanging.
The judge said Aziz was being prosecuted because he signed the execution orders against the merchants as a member of Saddam's Revolutionary Command Council.