The purpose of this study was to evaluate the effectiveness of full three‐dimensional (3D) gamma algorithm for spot scanning proton fields, also referred to as pencil beam scanning (PBS) fields. The difference between the full 3D gamma algorithm and a simplified two‐dimensional (2D) version was presented. Both 3D and 2D gamma algorithms are used for dose evaluations of clinical proton PBS fields. The 3D gamma algorithm was implemented in an in‐house software program without resorting to 2D interpolations perpendicular to the proton beams at the depths of measurement. Comparison between calculated and measured dose points was carried out directly using Euclidian distance in 3D space and the dose difference as a fourth dimension. Note that this 3D algorithm faithfully implemented the original concept proposed by Low et al. (1998) who described gamma criterion using 3D Euclidian distance and dose difference. Patient‐specific proton PBS plans are separated into two categories, depending on their optimization method: single‐field optimization (SFO) or multifield optimized (MFO). A total of 195 measurements were performed for 58 SFO proton fields. A MFO proton plan with four fields was also calculated and measured, although not used for treatment. Typically three different depths were selected from each field for measurements. Each measurement was analyzed by both 3D and 2D gamma algorithms. The resultant 3D and 2D gamma passing rates are then compared and analyzed. Comparison between 3D and 2D gamma passing rates of SFO fields showed that 3D algorithm does show higher passing rates than its 2D counterpart toward the distal end, while little difference is observed at depths away from the distal end. Similar phenomenon in the lateral penumbra was well documented in photon radiation therapy, and in fact brought about the concept of gamma criterion. Although 2D gamma algorithm has been shown to suffice in addressing dose comparisons in lateral penumbra for photon intensity‐modulation radiation therapy (IMRT) plans, results here showed that a full 3D algorithm is required for proton dose comparisons due to the existence of Bragg peaks and distal penumbra. A MFO proton plan with four fields was also measured and analyzed. Sharp dose gradients exist in MFO proton fields, both in the middle of the modulation and toward the most distal layers. Decreased 2D gamma passing rates at locations of high dose gradient are again observed as in the SFO fields. Results confirmed that a full 3D algorithm for gamma criterion is needed for proton PBS plan's dose comparisons. The 3D gamma algorithm is implemented by an in‐house software program. Patient‐specific proton PBS plans are measured and analyzed using both 3D and 2D gamma algorithms. For measurements performed at depths with large dose gradients along the beam direction, gamma comparison passing rates using 2D algorithm is lower than those obtained with the full 3D algorithm.PACS number: 87.53.Bn, 87.53.Jw, 87.55.de, 87.55.kd, 87.55.ne, 87.55.Qr