Globally, health research organizations are called upon to re-examine their policies and practices to more efficiently and effectively address current scientific and social needs, as well as increasing public demands for accountability. Through a case study approach, the authors examine an effort undertaken by the National Institute of Allergy & Infectious Diseases (part of the National Institutes of Health, Department of Health & Human Services, United States Government) to develop an evaluation system for its recently restructured HIV/AIDS clinical trials program. The challenges in designing, operationalizing, and managing global clinical trials programs are considered in the context of large scale scientific research initiatives. Through a process of extensive stakeholder input, a framework of success factors was developed that enables both a prospective view of the elements that must be addressed in an evaluation of this research and a current state assessment of the extent to which the goals of the restructuring are understood by stakeholders across the DAIDS clinical research networks.