Following a July 1988 unpublished order by Ayatollah Khomeini, several three-man commissions comprised of representatives of the Islamic Revolutionary Courts, the Revolutionary Prosecutor’s Office and the Ministry of Intelligence were formed in Tehran and the Provinces. Over a six-month period, these three-man commissions subjected thousands of political prisoners (from various leftist religious and secular groups), most of whom had already been tried and convicted, to formalized interrogation sessions. Between July 1988 and January 1989, thousands of political prisoners throughout Iran were summarily executed in the Islamic Republic's prisons. The executions were not announced publicly and families were informed of the executions weeks after they took place. Khomeini's alleged order was published in the memoirs of his presumptive successor, Ayatollah Montazeri, himself one of the founders of the Islamic Republic. Montazeri protested against the prison massacre and was sacked by Khomeini in retaliation in the spring of 1989.

During a press conference held in Tehran, on January 1st, 1981, Ayatollah Mohammad Beheshti, the President of Iran's Supreme Court, talked about the necessity to purge the Bar Association and discussed a defendant's right to counsel. Iran's Bar Association had issued several petitions against the absence of due process and human rights abuses in the post-revolutionary judicial system. Ayatollah Beheshti's statements illustrate the growing pressure on lawyers and human rights advocates in Iran in 1981.

Ayatollah Sadeq Khalkhali (1926-2004) was the first religious judge appointed by Ayatollah Khomeini to head the Islamic Revolutionary Tribunal on February 24th, 1979. He tried and sentenced to death numerous associates of the former regime, as well as a number of left wing activists in the Iranian Kurdistan and Turkmen-Sahra. He also headed the Anti-Drugs Islamic Revolution's Tribunal and sentenced to death scores of people charged with drug addiction or trafficking. His statement on the right to counsel was translated by Amnesty International ("Law and Human Rights in the Islamic republic of Iran," 1980, p.52)

Ayatollah Khomeini's televised speech of April 2, 1979, was a response to numerous protests by Iranian and international human rights organizations against the lack of due process in the Islamic revolutionary judicial system. Ayatollah Khomeini's approach clearly indicated that Iran's new leadership was rejecting the presumption of innocence, a pillar of the pre-revolutionary justice system, and that defendants were officially considered guilty before being convicted.