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PURPOSE Small animal PET scanners are widely used in current biomedical research. The study aimed to develop high efficiency and ultra-high resolution detectors that could be used to develop a small animal PET scanner with high sensitivity and spatial resolution approaching to its physical limit. METHODS 4 crystal arrays were fabricated and measured in this study. Crystal arrays 1 and 2 consisted of 38 × 38 GAGG and LYSO crystals of 0.4 × 0.4 × 20 mm3 size. Crystal array 3 consisted of 16 × 16 GAGG crystals of 0.3 × 0.3 × 20 mm3 size, and crystal array 4 consisted of 24 × 24 LYSO crystals 0.3 × 0.3 × 20 mm3 in size. The crystal arrays were dual-ended readouts using 8 × 8 SiPM arrays of 2 × 2 mm2 pixel area. The SiPM array was read-out using a signal multiplexing circuit to convert the 64 output signals into 4 position-encoding signals. The performances of the 4 detectors in terms of flood histogram, energy resolution, depth of interaction resolution and timing resolution were measured. RESULTS The GAGG detectors provided better flood histograms, ∼30% higher photopeak amplitude, ∼20% higher energy resolution, ∼12% worse DOI resolution and ∼15% worse timing resolution compared with LYSO detectors of the same crystal size. These 4 detectors provided DOI resolutions of <2 mm, energy resolutions of <22% and timing resolutions of <1.6 ns. All crystals of 0.4 × 0.4 × 20 mm3 and 0.3 × 0.3 × 20 mm3 could be clearly resolved if the crystal array was 1 mm smaller in the four sides than that in the SiPM array. CONCLUSIONS High DOI resolution PET detectors were developed using both GAGG and LYSO arrays with crystal sizes of 0.3 and 0.4 mm, respectively, and a length of 20 mm. The detectors can be used in the future to develop small animal PET scanners, especially dedicated mouse imaging PET scanners, which can simultaneously achieve high sensitivity and ultra-high spatial resolution. This article is protected by copyright. All rights reserved.