There has been a significant increase in the understanding of the molecular changes leading to malignant transformation, and cancer scientists and physicians are now at the dawn of another era in cancer therapeutics. The identification of new drug targets and potential biomarkers, and the development of molecular targeted therapies for use in oncology are moving rapidly forward. It is imperative that appropriate and speedy advances in clinical trial design accommodate these developments, as the traditional design of early phase trials for ‘standard’ anti‐cancer therapies may not necessarily be appropriate for these new agents. In this chapter, we discuss some of the challenges posed in early clinical development of novel targeted therapies. These include the redefining of trial endpoints such as maximum tolerated dose, dose limiting toxicity and radiological response and applying new concepts such as novel clinical trial design, maximum biological dose, use of surrogate tissue as a biomarker for drug effect, and prolonged disease stasis as a measure of clinical benefit. We review clinical studies of several classes of small molecule anticancer therapies to illustrate attempts to maximise the benefits of these non traditional methodologies and minimise the limitations in driving the field of molecular cancer therapeutics further forward.