A system, method and program product for determining parallelism of an ion beam using a refraction method, are disclosed. One embodiment includes determining a first test position of the ion beam while not exposing the ion beam to an acceleration/deceleration electrical field, determining a second test position of the ion beam while exposing the ion beam to an acceleration/deceleration electrical field, and determining the parallelism of the ion beam based on the first test position and the second test position. The acceleration/deceleration electrical field acts to refract the ion beam between the two positions when the beam is not parallel, hence magnifying any non-parallelism. The amount of refraction, or lateral shift, can be used to determine the amount of non-parallelism of the ion beam. An ion implanter system and adjustments of the ion implanter system based on the parallelism determination are also disclosed.