This article examines trends in Malaysia's civil courts which have, in cases of perceived conflict of jurisdiction with the Syariah courts, conferred jurisdiction on the latter, especially in cases involving would-be apostates from Islam. This trend is examined against the backdrop of the sodomy trial against opposition party leader, Anwar Ibrahim, who has had rejected his appeals to have the accusations made in 2008 heard in the Syariah court, where the evidentiary requirements would likely see the case thrown out. A comparison of these conflicts of jurisdiction points toward the politicisation of religion in Malaysia and its impact on religious minorities.