In recent years, a number of approaches have been applied to the problem of deformable registration validation. However, the challenge of assessing a commercial deformable registration system – in particular, an automatic registration system in which the deformable transformation is not readily accessible – has not been addressed. Using a collection of novel and established methods, we have developed a comprehensive, four‐component protocol for the validation of automatic deformable image registration systems over a range of IGRT applications. The protocol, which was applied to the Reveal‐MVS system, initially consists of a phantom study for determination of the system's general tendencies, while relative comparison of different registration settings is achieved through postregistration similarity measure evaluation. Synthetic transformations and contour‐based metrics are used for absolute verification of the system's intra‐modality and inter‐modality capabilities, respectively. Results suggest that the commercial system is more apt to account for global deformations than local variations when performing deformable image registration. Although the protocol was used to assess the capabilities of the Reveal‐MVS system, it can readily be applied to other commercial systems. The protocol is by no means static or definitive, and can be further expanded to investigate other potential deformable registration applications.PACS numbers: 87.19.xj, 87.56.Da, 87.57.nj