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Background: Exercise-induced laryngeal obstruction (EILO) is diagnosed by the continuous laryngoscopy during exercise (CLE) test. Whether or how much CLE test scores vary over time is unknown. This study aimed to compare CLE test scores in athletes over time, irrespective of respiratory symptoms and grade of laryngeal obstruction. Methods: Ninety-eight athletes previously screened for EILO were invited for a follow-up CLE test irrespective of CLE scores and respiratory symptoms. Twenty-nine athletes aged 16–27 did a follow-up CLE test 3–23 months after the baseline test. Laryngeal obstruction at the glottic and supraglottic levels was graded by the observer during exercise, at baseline and follow-up, using a visual grade score (0–3 points). Results: At baseline, 11 (38%) of the 29 athletes had moderate laryngeal obstruction and received advice on breathing technique; among them, 8 (73%) reported exercise-induced dyspnea during the last 12 months. At follow-up, 8 (73%) of the athletes receiving advice on breathing technique had an unchanged supraglottic score. Three (17%) of the 18 athletes with no or mild laryngeal obstruction at baseline had moderate supraglottic obstruction at follow-up, and none of the 3 reported exercise-induced dyspnea. Conclusions: In athletes with repeated testing, CLE scores remain mostly stable over 3–24 months even with advice on breathing technique to those with EILO. However, there is some intraindividual variability in CLE scores over time. Trial registration: ISRCTN, ISRCTN60543467, 2020/08/23, retrospectively registered, ISRCTN – ISRCTN60543467: Investigating conditions causing breathlessness in athletes.