Diagnosis, treatment planning and prognosis may be improved by combining functional data with anatomic location via PET/CT dual-modality image registration. The aim of this work is to reveal the spatial accuracy, reliability and speed of registration techniques used in GeminiTM PET/CT Imaging System, as a part of quality assurance program for clinical and research applications. A multi-layer alignment bearing source device was used to validate PET/CT intrinsic alignment, as well as a Rando a Man phantom. A series of known transformations were performed to simulate different misalignment between PET and CT images. Two semi-automated registration techniques used to correct misalignment were assessed and compared quantitatively by measuring absolute distances between the centroids of corresponding fiducial markers in the registered volumes. Comparisons between independent and cross fiducial localization indicate that fused PET/CT is superior to visual correlation of PET and CT individually in identifying registration errors. The experimental and theoretical findings confirm that PET/CT hybrid system can produce robust intrinsic image alignment and accurate PET/CT image registration with careful user interaction. The maximum spatial error in our experiments is below 4 mm, and is better than the spatial resolution of the PET scanner used. This is considered to be sufficient for most PET/CT applications.