Malaysia’s Shariah court system long predates the country's Independence in 1957 and has since undergone a series of developments. Yet the Shariah court’s jurisdiction remains limited by the Parliament and the Federal Constitution. This limited jurisdiction has triggered an on-going conflict between Shariah courts and civil courts. This article discusses the jurisdiction of Shariah court prior to and after the landmark amendment inserting Article 121 (1A) into the Malaysian Federal Constitution. It also discusses the challenges faced by the Shariah courts within and outside the system. This article suggests that the present jurisdiction of the Shariah courts should be reviewed, and that the civil courts should not interfere with the jurisdiction that has been awarded to the Shariah courts, even if that jurisdiction is only implied. This article ends with a suggestion that a Special court should be set up to adjudicate cases pertaining to Islamic law but involving parties of different faiths.