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GATE (Geant4 Application for Tomographic Emission) simulation toolkit has become a well validated toolkit for the simulation of SPECT and PET systems. A very important feature of GATE is that it allows modelling of time-dependent phenomena. In addition, complex voxelized object such as realistic anthropomorphic or small animal phantoms can be used as emission sources. In this work two small field of view scanners have been evaluated experimentally, modelled in GATE and mice studies have been simulated using MOBY mouse phantom. Two scanners have been simulated: The first one is a mouse sized gamma camera (field of view is 5 times 10cm) that is based on two Hamamatsu H8500 PSPMTs, a NaI pixelized scintillator and a tungsten collimator with hexagonal parallel holes. The system has been modelled in GATE and good agreement has been found between simulation and experimental results. MOBY mouse has been introduced as a voxelized source and planar and tomography simulations were carried out. The second small animal PET scanner has four heads which are equipped with a H8500 PSPMTs and a pixelated LYSO scintillator. System's geometry has been modelled in GATE. The results of both systems simulation and comparison between simulation and experimental data are presented. In addition, mouse bone scans were simulated both for SPECT and PET and tomographic image are derived. The presented methodology is aimed to provide all necessary tools in order to perform optimized simulations of small animal emission tomography scans.