The development of new technologies in radiation therapy has made it possible to introduce more sophisticated techniques that can deliver the prescribed dose with more conformation and accuracy and to apply dose escalation protocols without increasing the risk of healthy tissue damage. This has consented the simultaneous delivery of different dose levels to different parts of the target, making it possible to boost those tumour sub-volumes that are considered more radio resistant. The use of PET for radiotherapy planning purposes has become increasingly important in the last few years, because of its ability to provide valuable biologic and functional data. PET imaging can affect the treatment strategy definition and improve the target delineation and the assessment of therapy response. The most attractive aspect is the perspective to deliver differential doses inside target volumes for areas of different biologic behaviour based on functional imaging, moving closer to the goals of biologically conformal radiation therapy. Each single step of PET/CT-guided radiotherapy workflow, needs to be performed following high standard procedures, within a rigorous and appropriate quality assurance protocol to minimize the sources of errors and to maximize the efficacy of PET imaging in radiation therapy, ensuring safe and effective use of the technology. The present paper focuses on aspects concerning the use of PET/CT in radiation treatment process, with the aim to delineate different possible approaches to its clinical application and to highlight the critical aspects of the various subprocesses.