GATE (Geant4 Application for Tomographic Emission) was used to perform a Monte-Carlo simulation of a fully 3D clinical PET scanner. The Philips Allegro PET system was simulated in order (a). to allow a detailed study of the parameters affecting the system’s performance under various imaging conditions, and (b). to further validate the use of GATE for the simulation of clinical PET systems. A model of the detection system and its geometry was developed. The simulation of count rate related performance characteristics of the scanner was facilitated through the development of a dead time model to describe data flow and data loss at the level of detected single events and coincidences. The developed system design and associated dead time model were validated by comparing simulated with experimental measurements obtained with the Allegro PET system. These measurements included the use of point as well as distributed sources, allowing us to determine spatial resolution, scatter fraction, sensitivity, and count rate performance based on the NEMA NU2-1994 protocols. Using the NEMA phantom, simulated single and coincidence count rates were within 5% of the corresponding measured rates throughout a wide range of activity concentrations. Scatter fraction and random coincidences were also measured and combined with total recorded coincidence rates in order to validate simulated NEC rate curves. Differences between simulated and measured NEC curves were found to be within 7% and can be attributed to the approximations in the simulation including no photomultiplier tube response, gantry surroundings or the effects of pulse pile up in the modeling of the electronics. These results support an accurate modelling of the Philips Allegro PET system using GATE in combination with an appropriate dead time model.