Recently, Japan has put great effort into concluding regional trade agreements (RTAs), which has resulted in a number of so-called economic partnership agreements (EPAs). Not surprisingly, the conclusion of RTAs is not the end of the story. Japan will soon face the challenge of securing effective execution of these agreements. In this context, institutional arrangements are inevitable for the effective functioning of RTAs: every RTA needs proper organization to ensure its effective operation and RTAs have to adjust themselves to the subsequent changes in circumstances. Problems relating to these issues become reality soon after each RTA comes into effect, and this will be the more the case as time goes by. However, there has been little empirical research on this issue. This is partly because RTAs are so diverse that a meaningful comparison is difficult to make; partly because the dispute settlement mechanism attracted (disproportionately) attention; and partly because there is little question about consistency with the WTO Agreements since the WTO Agreements do not provide clear regulations on institutional arrangements of RTAs. Thus, this paper tries to clarify the role of institutional arrangements in the EPAs concluded by Japan, and then evaluate them by looking into related provisions that deal with changes that occurred after the EPA comes into effect. The purpose of this paper is to take initial steps toward empirical analysis of institutional arrangements for these RTAs, which indicates how they should be designed for each RTA according to its specific features. Particularly, this paper focuses on several core provisions that regulate the institutional operation of RTAs: (1) provisions relating to the relationship with other agreements; (2) provisions relating to the organization of RTAs, including their management and decision-making; and (3) provisions relating to later change to RTAs, including amendment, accession, and termination. These three categories cover both "internal aspects" of the institutional arrangement (how the RTA manages its internal functioning), as well as its "external aspects" (how the RTA keeps its integrity against other instruments). Following Chapter I that specifies problems to be addressed, Chapter II of this paper clarifies methodology of the analysis. Chapter III conducts multi-dimensional comparison of Japan's EPAs, which is summarized in Chapter IV, the concluding chapter. The following is a summary of our multi-dimensional comparisons. First, with regard to the relationship with other agreements, the majority of Japan's EPAs are characterized by an explicit deference to the WTO Agreements by means of providing provisions that give precedence to the Agreements. In contrast, there is considerable ambiguity with regard to the relationships with agreements other than the WTO Agreements. Secondly, as regards management and decision-making, Japan's EPAs are typified by flexibility. In other words, Japan's EPAs leave almost all issues open for consultation among the contracting parties. While this approach generates from Japanese negotiators' concern about logistic burdens, we should note that flexibility creates uncertainty in the systems, which may hinder orderly management of the EPAs. Third and lastly, with regard to later adjustments, Japan's EPAs are, on the one hand, characterized by a marked flexibility for amendment, and a lack of flexibility for accession on the other. It does not seem balanced to deny any opportunity for accession, in view that this plays a similar role to amendment in certain situations.