New discoveries in basic science are creating extraordinary opportunities to design novel biomedical preventions and therapeutics for human disease. But the clinical evaluation of these new interventions is, in many instances, being hindered by a variety of legal, regulatory, policy and operational factors, few of which enhance research quality, the safety of study participants or research ethics. With the goal of helping increase the efficiency and effectiveness of clinical research, we have examined how the integration of utilization-focused evaluation with elements of business process modeling can reveal opportunities for systematic improvements in clinical research. Using data from the NIH global HIV/AIDS clinical trials networks, we analyzed the absolute and relative times required to traverse defined phases associated with specific activities within the clinical protocol lifecycle. Using simple median duration and Kaplan-Meyer survival analysis, we show how such time-based analyses can provide a rationale for the prioritization of research process analysis and re-engineering, as well as a means for statistically assessing the impact of policy modifications, resource utilization, re-engineered processes and best practices. Successfully applied, this approach can help researchers be more efficient in capitalizing on new science to speed the development of improved interventions for human disease.