Imaging of biological processes using specific molecular probes allows exploration of the mechanism of action and efficacy for new therapies. This molecular imaging has made use of modalities including single photon emission computed tomography (SPECT), positron emission tomography (PET), magnetic resonance imaging (MRI), and optical techniques. Molecular imaging can be used to explore many of the hallmarks of cancer biology, including angiogenesis, proliferation, tissue invasion, evasion of apoptosis, and self-sufficiency in growth signals. Since many of these aspects of cancer biology are in turn the targets of novel therapies in development, molecular imaging techniques have great potential to inform trials of these new agents. The high cost of clinical drug development mandates the optimisation of early phase trial design to maximise the collection of evidence for efficacy and proof of mechanism, endpoints which have, in a number of examples, already been provided by molecular imaging. The variety provided by novel chemistry, and the availability of isotopes with varying physical properties, particularly suits PET imaging as a functional modality for application in clinical trials.