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In this paper, we present the results from a design study for an ultra-high resolution SPECT system with various aperture designs. The system uses a recently developed ultrahigh resolution gamma camera based on an intensified Electron- multiplying Charge Coupled Device (EMCCD) sensor. It provides an intrinsic spatial resolution of < 60 mum and a high signal-to-noise ratio for imaging the 27-35 keV photons emitted by 1-125. The goal of present work is to optimize the multiple- pinhole aperture design for a stationary 4 headed SPECT system. The system is equipped with a variable aperture system that allows a large number of different aperture configurations to be used. In this study, we used the resolution-variance tradeoff as a performance index for selecting appropriate apertures for several imaging scenarios. A large number of apertures were compared with Monte Carlo simulations and experimental measurements.