MicroPET is a low-cost, high-resolution positron emission tomography (PET) scanner designed for imaging small animals. MicroPET operates exclusively without septa, acquiring fully three-dimensional (3-D) data sets. The performance of the projection-reprojection (3DRP), variable axial rebinning (VARB), single slice rebinning (SSRB), and Fourier rebinning (FORE) methods for reconstruction of microPET data were evaluated. The algorithms were compared with respect to resolution, noise variance, and reconstruction time. Results suggested that the 3DRP algorithm gives the best combination of resolution and noise performance in 9 min of reconstruction time on a Sun UltraSparc I workstation. The FORE algorithm provided the most acceptable accelerated method of reconstruction, giving similar resolution performance with a 10%-20% degradation in noise variance in under 2 min. Significant degradation in the axial resolution was measured with the VARB and SSRB methods, offsetting the decrease in reconstruction time achieved with those methods. In-plane angular mashing of the 3-D data before reconstruction led to a 50% reduction in reconstruction time but also introduced unacceptable tangential blurring artifacts. This thorough evaluation of analytical 3-D reconstruction techniques allowed for optimal selection of a reconstruction method for the diverse range of microPET applications.