This article seeks to analyse two possible legal bases on which jurisdiction clauses included in Regional Trade Agreement (RTAs) may be enforced in disputes before the World Trade Organization (WTO), namely, the application of RTA jurisdiction clauses as applicable law in WTO disputes, and that as WTO tribunals' inherent powers. It will be argued that the applicability RTA jurisdiction clauses in WTO disputes is originally a matter of applicable law. However, there are no provisions in WTO law that either fully confirm or entirely eliminate such an application. Thus, the applicability of RTA jurisdiction clauses cannot be decisively verified from the applicable law perspective. In this context, it is natural that whether they can be enforced in WTO disputes largely depends on the discretion and willingness of WTO tribunals to do so. From this understanding, the article then takes into consideration two important factors, namely, inherent powers of WTO tribunals, and the requirements set out in the Dispute Settlement Understanding (DSU) to assess how these factors, as well as the interaction between them may constrain or drive the application of RTA jurisdiction clauses in WTO disputes. It appears that even though equipped with the inherent power to decide their own jurisdiction, WTO tribunals cannot enforce RTA jurisdiction clauses because such enforcement would be inconsistent with the key provisions of the DSU.