The purpose of the study was to determine the incidence rate of injuries and the risk of injury on first-year students of the Human Movement Sciences Program from the University of Costa Rica during the school year 2014. In this prospective study, 47 students voluntarily completed an informed consent and a self-report questionnaire to determine injuries and physical activity habits. Participants were instructed that every Monday of the semester should report any injury that occurred during the previous week, and to make a doctor's appointment for an accurate diagnostic. Results indicated that 31.8% of the first-year students (80% women, 30% men) entered the program already injured (p < 0.001). During the follow-up year, 59.5% of the student population reported a new injury. There were 37 new lesions, 24 (64.9%) in women and 13 (35.1%) in men, being the knee and thigh the most frequent injuries. These lesions occurred mainly in the extracurricular context. The injury risk for the population was 0.79 and the incidence rate of 2.00 injuries/1000-h of exposure. In conclusion, the first-year male and female student population of the Human Movement Sciences Program at the University Costa Rica is vulnerable to injuries in the lower body, with a greater number of injuries in the second semester of the year. Longitudinal studies are needed to determine the evolution and care of injuries throughout the program.