This work presents a method for CT and PET image registration, and multi-modal analysis, to optimize radiotherapy planning in lung cancer treatment. The method relies on an image registration technique based on fiducial external markers to realign, spatially, PET images with the CT spatial reference system. The method was set up for clinical use in radiotherapy, allowing minimal modifications to be introduced in the management of patients undergoing radiation treatment. The accuracy of the registration technique was evaluated on patient studies in terms of Target Registration Error and was found to be less than 6.40 mm. The method was applied in the treatment planning of five patients affected by non-small-cell lung cancer, revealing the usefulness of PET/CT integration in delineating the extension of both the tumor mass and the tissues involved in the neoplastic process. Moreover, the functional information provided by PET often led to alterations in the treatment planning, changing the size and/or direction of radiation portals. The proposed method for PET/CT integration has been confirmed as being useful for optimizing radiotherapy planning in lung cancer treatment.