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The Balance Error Scoring System (BESS) is a commonly used concussion assessment tool. Recent studies have questioned the stability and reliability of baseline BESS scores. The purpose of this longitudinal prospective cohort study is to examine differences in yearly baseline BESS scores in athletes participating on an NCAA Division-I football team. NCAA Division-I freshman football athletes were videotaped performing the BESS test at matriculation and after 1 year of participation in the football program. Twenty-three athletes were enrolled in year 1 of the study, and 25 athletes were enrolled in year 2. Those athletes enrolled in year 1 were again videotaped after year 2 of the study. The paired t-test was used to assess for change in score over time for the firm surface, foam surface, and the cumulative BESS score. Additionally, inter- and intrarater reliability values were calculated. Cumulative errors on the BESS significantly decreased from a mean of 20.3 at baseline to 16.8 after 1 year of participation. The mean number of errors following the second year of participation was 15.0. Inter-rater reliability for the cumulative score ranged from 0.65 to 0.75. Intrarater reliability was 0.81. After 1 year of participation, there is a statistically and clinically significant improvement in BESS scores in an NCAA Division-I football program. Although additional improvement in BESS scores was noted after a second year of participation, it did not reach statistical significance. Football athletes should undergo baseline BESS testing at least yearly if the BESS is to be optimally useful as a diagnostic test for concussion.