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68Ga is one of the non-conventional nuclides that are being used in preclinical imaging. One disadvantage of 68Ga versus 18F is its larger positron range, which deteriorates the effective spatial resolution and the overall image quality. In this work we present a performance evaluation of the ARGUS small-animal positron emission tomography (PET) scanner for two positron emitters, 68Ga and 18F. These experiments followed the procedure based on the National Electrical Manufacturers Association (NEMA) NU 4-2008 standard. We show how the use of 68Ga may affect the NEMA performance of the system in terms of image quality and spatial resolution. The recovery coefficients (RC) measured in the image-quality phantom ranged from 0.17 to 0.72 for 68Ga and from 0.28 to 0.92 for 18F, using iterative image reconstruction methods and applying all corrections. Under the same conditions the image noise (%STD) in a uniform region was 17.0% for 68Ga and 15.1% for 18F. The respective spillover ratios (SOR) were 0.13 and 0.09 in air, and 0.21 and 0.12 in water. Attenuation correction yielded an improvement of the SOR close to 50% for both radionuclides in the air-filled region. This work evaluates the image reconstruction methods and corrections available in the ARGUS PET for 68Ga and 18F to assess the influence of their physical properties on the NEMA parameters.