Al-Ubaydi represented Hussein and the ousted Iraqi leader's half-brother, Barzan Ibrahim. They are charged with killing more than 140 people in the town of Al-Dujayl in 1982.
Al-Ubaydi's body was found on the street near the impoverished Shi'ite neighborhood of Sadr city.
Khalil al-Dulaymi, Hussein's chief defense lawyer, said in an interview with Radio Free Iraq that killers are on a "rampage" in Iraq.
"The death of colleague Khamis al-Ubaydi, deputy head of the defense team, is not the only instance," al-Dulaymi said. "It is one in a series of assassinations carried out by militant militias that have come from Iran in the wake of occupation. They are now on the rampage. The first and foremost party responsible for the death of colleague al-Ubaydiand five other colleagues gunned down are these terrorist militias and also the Interior Ministry. They take turns."
Al-Ubaydi is the third defense attorney to be assassinated since the trial against Hussein and the other seven defendants began in October.