The case challenging the inclusion of the kadhi courts in the Constitution was filed six years ago by 26 church leaders.
This was when the Bomas draft was under debate and the clerics were contesting the inclusion of the Muslim courts in the proposed law.
The case was brought before the Constitutional Court by a group led by the Presbyterian Church of East Africa (PCEA) moderator, Rev Jesse Kamau.
Others included African Inland Church bishop Silas Yego, Bishop Margaret Wanjiru of Jesus is Alive Ministries, former PCEA moderator David Githii, Bishop Arthur Kitonga of the Redeemed Gospel Church and Bishop Boniface Adoyo of the Nairobi Pentecostal Church.
Attorney General Amos Wako and the Constitutional Review Commission of Kenya (CKRC) were listed as respondents.
The suit, which was filed on July 12, 2004, was amended on November 30, the same year, with a further amendment on January 31, 2005.
According to the church leaders, the inclusion of the kadhi courts in the Constitution amounted to favouring one religion over the others practised in the country.
Their case was supported by the Hindu Council of Kenya, which said that religious courts should not be made part of the Constitution.
However, the AG asked the court to dismiss the case, arguing that it had no jurisdiction to grant the orders sought.
Among the people who testified was High Court judge Abida Ali Aroni, who was then the vice chairperson of the CKRC.
She swore an affidavit and gave 30 reasons as to why the court should dismiss the case.
But yesterday the three-judge bench consisting of appeal judge John Nyamu and High Court judges Mathew Anyara Emukule and Roselyne Wendoh found that the inclusion of the kadhi courts in the constitution was discriminatory.
They however did not mention whether the provision should be in the proposed constitution.