The acoustic startle reflex (ASR) is an intense reaction that involves the contraction of muscle groups in response to an unexpected stimulus. We proposed that an ASR measurement may be used to select physical characteristics among healthy people, including athletes. To find the relationship between the ASR and physical conditioning level, we designed a study to perform ASR measurements, anthropometric measurements, neuromuscular conjugation exercises, strength test, and flexibility test. We studied young adults into 4 groups: male-control, male-athlete, female-control, and female-athlete. Our results showed how the startle amplitude was decreased in athletes compared with controls. In most of the anthropometric parameters, there were differences attending to gender in control groups, but these differences diminished in athletes. In addition, some fitness values were correlated with the latency of the muscle response and with the prepulse inhibition. This study demonstrates that regular practice of a sport, aside from causing changes in common fitness variables, also promotes changes in ASR parameters. In some way, the intense body training stimulates the brain reorganization to enhance some responses related to adapt the ASR. With this study, we are opening a field for those interested in finding out new instruments to discriminate athletes.