Subepiglottic cysts (SECs) are an infrequent cause of upper respiratory tract noise and exercise intolerance in horses. They may also be associated with no clinical signs and be an incidental finding during routine upper airway endoscopy. The aim of this study was to assess the effect on performance of horses undergoing surgical removal of SECs. The case records of 15 horses (1995–2009) diagnosed with SECs were retrieved. Eleven (73%) of the 15 horses included in the study were Thoroughbred racehorses. Eleven (73%) of the 15 horses had no preoperative clinical signs related to the SECs, with the remaining 4 (27%) having a respiratory noise (n = 4), nasal discharge (n = 1), difficulty swallowing (n = 1) or a cough (n = 1). Endoscopic examination in the standing horse was diagnostic in 93% (n = 14) of horses. Nine (82%) of the 11 Thoroughbred horses were yearlings, of which only one horse (11%) presented with clinical signs consisting of a respiratory noise and nasal discharge. Four of the 11 (36%) Thoroughbred horses were found to have concurrent epiglottic entrapment. Surgical removal was successful in all cases. Eight of the 11 (73%) Thoroughbred horses in this study raced following SEC removal. The majority of SECs are identified during routine endoscopic examinations and are not associated with clinical signs. The prognosis following surgical removal of SECs is good and future performance does not appear to be affected.