Introduction: To examine the various processes involved and to assess their effects on the accuracy of proton therapy. Materials and methods: Proton therapy involves several processes: (1) Beam commissioning. (2) CT of patient to obtain the anatomical information of the patient. (3) Contouring of the tumors and organs at risks from the CT images. (4) Treatment planning to determine the beam configurations, the aperture and compensators, and the beam weightings, satisfying a specific set of dose-volume constraints. (5) Output factor measurements for each field. (6) Patient setup verification with image guidance. (7) Dose delivery. (8) Neutron dose and proton RBE at the distal edge. Within each step, there are several sub- processes that may contribute to the uncertainty in the treatment. By analyzing each of the sub-processes within each process, we estimated an uncertainty to each sub-process and/or an uncertainty on the proton range (in millimeter). A total uncertainty in dose delivery and the location of the distal edge can be estimated. Results: Examples of the uncertainties assessed for the various processes are : (1) ±1.5%; (4) ±3.0%, and 1-3mm; (5) ±2.0%; (6) ±2 mm; (7) ±2.0%, ±2mm. The uncertainties in (2), (3)and (8) neutron dose strongly depend on the location and type of the tumor. The proton RBE value at the distal edge is still debatable. The overall uncertainty in proton therapy is at least ±4.5% and ±4 mm (by adding the various uncertainties in quadrature), without consideration of processes (2), (3) and (8).Discussion: Due to the complexity in proton therapy, it is far more complicated to assess the accuracy in proton therapy than that for photon therapy. We showed that the accuracy in proton therapy is at least ± 4.5% in dose delivered to a tumor with an uncertainty of ±4mm to the distal edge of the SOBP.