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Objective: To describe the location and severity of pain during Functional Movement Screen (FMS) testing in junior Australian football players and to investigate its effect on FMS composite score and injury risk., Design: Prospective cohort study., Methods: Junior male Australian football players (n = 439) completed preseason FMS testing. Pain location and severity (on a 0-to-10 numeric pain-rating scale [NPRS]) were assessed for painful subtests. The FMS composite score was calculated using 3 scoring approaches: "traditional," a score of zero on painful subtests; "moderate," a score of zero on painful subtests if an NPRS pain severity was greater than 4; and "raw," did not adjust painful FMS subtest scores. Players were monitored throughout the competitive season and considered injured when 1 or more matches were missed due to injury., Results: One hundred seventy players reported pain during FMS testing. The pain-scoring approach affected mean composite score values (raw, 14.9; moderate, 14.5; traditional, 13.6; P <.001). Sixty-eight percent of pain was mildly severe (NPRS of 4 or less). Back pain (50%) was more common than upper-limb (24%) or lower-limb (26%) pain ( P <.001). Upper-limb pain was associated with a small increase in injury risk (hazard ratio = 1.59, P = .023). No other FMS pain location influenced injury risk, nor did pain severity ( P >.280). The FMS composite score was not associated with injury risk, regardless of pain-scoring approach ( P ≥.500)., Conclusion: Pain was common during FMS testing in junior Australian football players and had a notable effect on the FMS composite score, but minimal effect on subsequent injury risk. J Orthop Sports Phys Ther 2020;50(2):75-82. Epub 17 Sep 2019. doi:10.2519/jospt.2020.9168 .