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Micro-pinhole SPECT system with conventional multiple-head gamma cameras has the advantage of high magnification factor for imaging of small animals such as rodents. However, several geometric factors should be calibrated to obtain the SPECT image with good image quality. We developed a simplified geometric calibration method for rotating triple- head pinhole SPECT system and assessed the effects of the calibration using several phantom and rodent imaging studies. Trionix Triad XLT9 triple-head SPECT scanner with 1.0 mm pinhole apertures were used for the experiments. Approximately centered one point source was scanned to track the angle- dependent positioning errors. The centroid of point source was determined by the center of mass calculation. Axially departed two point sources were scanned to calibrate radius of rotation from pinhole to center of rotation. To verify the improvements by the geometric calibrations, we compared the spatial resolution of the reconstructed image of Tc-99m point source with and without the calibration. SPECT image of micro performance phantom with hot rod inserts was acquired and several animal imaging studies were performed. Exact sphere shape of the point source was obtained by applying the calibration and axial resolution was improved. Lesion detectability and image quality was also much improved by the calibration in the phantom and animal studies. Serious degradation of micro-pinhole SPECT images due to the geometric errors could be corrected using a simplified calibration method using only one or two point sources.