The growing pipeline of candidate drugs for cystic fibrosis (CF) is challenging clinical trial research. There has been a shift from evaluating drugs aimed at treating the secondary manifestations of CF to evaluating drugs targeted toward the primary prevention of chronic lung disease. As CF is an orphan disease, there is a fundamental need to assess new therapies efficiently and accurately by mechanisms that best use the number of available patients. This need can be addressed with the continued advancement and refinement of CF outcome measures. We begin by presenting an overview of the outcome measures currently used in CF clinical studies, defined and categorized in terms of one of the three main classes of endpoints: clinical efficacy measures, surrogate endpoints, and biomarkers. To move forward efficiently, clinical research in CF is dependent on the development of new outcomes able to capture biologic and clinical response to novel therapeutic approaches. We conclude with a discussion of the criteria by which all new outcome measures should be evaluated. A systematic, rigorous approach to outcome measure development is needed to provide the tools necessary for evaluating new therapies and moving drugs out of the pipeline and into the CF clinic.