The purpose of this study was to develop fully 3D image reconstruction techniques for pinhole SPECT imaging with our Micro-SPECT system. Our studies involve in the derivation of projection operators, analysis of the sampling characteristics of pinhole SPECT imaging in Radon space, development of effective geometric calibration method for system misalignment, and 3D image reconstruction development and implementation with quantitative degrading compensation for pinhole SPECT with both circular and helical scan. The performances of pinhole SPECT imaging were evaluated using computer simulations and experiments with the Ultra-Micro Hot-Spot phantom, Ultra-Micro Defrise phantom and small-animal imaging. The results from the computer simulations and phantom imaging experiments indicate that the statistically-based iterative algorithms with quantitative compensation provide overall image quality improvement, and the system resolution is significantly recovered for quantitative imaging. The helical pinhole SPECT improves the axial field-of-view (FOV) as compared with the standard pinhole SPECT with circular-orbit scan. The mouse bone imaging experiment shows that the helical pinhole SPECT imaging also provides decent high-resolution whole-body small animal imaging. In conclusion, we have successfully developed a set of valid fully 3D image reconstruction techniques for single-pinhole SPECT imaging. These techniques can be easily extended to multi-pinhole SPECT imaging.