Exposure to HZE particles produces changes in central nervous system function which may, in turn, affect cognitive performance. The evaluation of the effects of exposure on behavior requires the use of animal models, which can differ in validity and reliability. Also, the disruption of performance can reflect deficits in different factors which can influence behavior: sensory, motor, or integrative components. The present review considers the procedures which must be employed to study the effects of exposure to HZE particles and protons on cognitive performance and how these may be influenced by the use model systems.