Molecular imaging tools such as Positron Emission Tomography (PET) are increasingly being used in the drug development process. The unrivaled sensitivity of PET coupled with a solid experience in developing highly targeted molecular probes makes this technique a very valuable tool at all stages from pre-clinical development to the clinical phases. Positron emitting tracers allow us to measure, quantitatively, molecular processes and interactions between a candidate drug and its molecular targets. This information can save time and money by directing development towards the most promising compounds and excluding molecules with unfavorable properties that would otherwise only be recognized as failures in latter stages of the process. In this paper we review the application of positron emitting tracers in the pre-clinical stages of the drug development process in the areas of oncology, cardiology, neurosciences and inflammatory diseases. PET tracers provide an important support for drug development in the areas of: discovery of new drug targets, clarification of pathophysiology, identification of potential drug candidates and validation of drug effectiveness, as well as the evaluation of pharmacokinetic and pharmacodynamic parameters in vivo.