Managing large, complex urban transportation systems involves numerous stakeholders because of decentralized ownership and operation of distinct pieces of the physical network and services. To deliver better service to users, many urban regions are adopting technological and operational solutions, both of which necessitate interaction among the decentralized organizations. This research applies systems engineering analysis techniques - design structure matrix and clustering - to improve efficiency and effectiveness of organizational interactions between agencies as they deploy intelligent transportation systems (ITS) and attempt to integrate their operations. Specifically, this paper examines the application of clustering to the institutional structure set forth by the regional ITS architecture for metropolitan Seattle, Washington. Clustering of Seattle area organizations noted previously unidentified multilateral relationships that offer potential for more efficient interagency interactions and, ultimately by extension, delivery of more effective transportation services to users.