Fear conditioning is a frequently used paradigm for assessing learning and memory in rodents. Traditionally researchers have relied upon scoring of fear-related behavior by human observation, which can be difficult and subjective and thus vary among investigators. The goal of this study was to evaluate the ability of EthoVision tracking software (Noldus Information Technology Inc.) to reliably and accurately score fear-related behavior in mice. Specifically, we were interested in its ability to accurately track mice and score immobility as a fear-related behavior during contextual and cued fear conditioning. Contextual and cued fear conditioning were performed in modified PhenoTyper chambers (Noldus Information Technology Inc.) fitted with grid floors to deliver a scrambled foot shock. Our results demonstrate that we have identified parameters in EthoVision that can accurately track mice and be used for automated scoring of immobility that is nearly identical to scoring by human observation. Together, EthoVision software and the modified PhenoTyper chambers provide an excellent system for the reliable and accurate measurement of fear-related behavior in a high-throughput manner.