Functional training is task or occupation specific and for the combat athlete may include a substantial amount of agility training. Agility training has recently been instituted in several combat athlete communities in hopes of improving combat performance as well as general fitness. Foot-speed and agility drill training has been demonstrated to improve performance in agility tests whereas traditional linear or “non-skilled” exercise does not appear to improve performance on such tests. Agility training may also improve cognitive performance. In animal models, while exercise alone offers neurological benefits, many studies suggest a greater benefit from agility training. Skilled exercise results in synaptogenesis in the motor cortex and cerebellum whereas unskilled motor movement training demonstrates no ability to change the number of synapses in these regions. PURPOSE: The purpose of this study was to determine how substituting physical agility training for traditional linear running influences physiological performance (physical fitness) and cognitive performance (mental fitness, specifically memory and vigilance.) METHODS: 22 subjects undergoing military technical training were divided randomly into two groups for 6 weeks of physical training. One group participated in standard military technical school physical training, which consisted of calisthenics and moderate distance linear running. A second group duplicated the duration and volume of exercise of the first group, but used agility training as their primary mode of exercise. The agility training consisted of ladder drills, hurdle crossings, dot/footspeed drills, and directional force change drills. Prior to and immediately following the 6 weeks of training, all subjects completed a physical and cognitive battery consisting of serum cortisol, V̇o2max, vertical jump, reaction time, Illinois agility, body composition, declarative memory, visual vigilance, dichotic listening, and working memory tests. RESULTS: There were no significant differences between or within groups for any of the measured variables. However, there were strong trends toward the agility group improving more over the training period than did the traditional group on V̇o2max, body composition, Illinois agility time, dichotic listening, and visual vigilance. CONCLUSIONS: Physical agility training is as effective, or more effective, as traditional linear running in enhancing general physical fitness. Further, it is likely more effective than linear running in enhancing specific measures of physical and cognitive performance, such as physical agility, memory and vigilance. PRACTICAL APPLICATIONS: Physical agility training should be a central component of military physical training and most sports training. It may also be a beneficial tool for improving both mental and physical fitness in the general population as well.