New therapeutic strategies are targeting correction of the basic defect in cystic fibrosis (CF) disease. In fact, completion of the first successful clinical drug trials now signals the start of a new era in CF therapy. Many promising drug candidates are emerging into the clinical drug pipeline. However, their translation from the bench to the bed side is challenged by the lack of accurate and reliable biomarker assays that allow testing for their clinical efficiency and safety in early clinical trials. It is surprising that despite the availability of modern equipment and technologies relatively little effort has been directed towards innovative approaches to exploit our pathophysiological understanding of CF disease for the design of novel assays that allow in vivo assessment of CFTR dysfunction as the measurable correlate of the basic defect of CF disease. This lack of adequate outcome measure is now gaining increased attention, and first studies are being initiated to screen larger CF patient cohorts for biological markers that can be used as a potential measure of drug response. This paper reviews currently available in vivo tests, highlighting new methods and their potential use as early in vivo markers for therapeutic investigations. Finally, key criteria of the validation process that needs to be addressed before new biomarker assays can be introduced into clinical trials are discussed.