Exercise induced intermittent dorsal displacement of the soft palate (DDSP) is a common cause of airway obstruction and poor performance in racehorses. The definite etiology is still unclear, but through an experimental model, a role in the development of this condition was identified in the dysfunction of the thyro-hyoid muscles. The present study aimed to elucidate the nature of this dysfunction by investigating the spontaneous response to exercise of the thyro-hyoid muscles in racehorses with naturally occurring DDSP. Intramuscular electrodes were implanted in the thyro-hyoid muscles of nine racehorses, and connected to a telemetric unit for electromyographic monitoring implanted subcutaneously. The horses were recruited based on upper airway function evaluated through wireless endoscopy during exercise. Five horses, with normal function, were used as control; four horses were diagnosed as DDSP-affected horses based on repeated episodes of intermittent dorsal displacement of the soft palate. The electromyographic activity of the thyro-hyoid muscles recorded during incremental exercise tests on a high-speed treadmill was analyzed to measure the mean electrical activity and the median frequency of the power spectrum, thereafter subjected to wavelet decomposition. The affected horses had palatal instability with displacement on repeated exams prior to surgical implantation. Although palatal instability persisted after surgery, only two of these horses displaced the palate after instrumentation. The electromyographic traces from this group of four horses showed, at highest exercise intensity, a decrease in mean electrical activity and median power frequency, with progressive decrease in the contribution of the high frequency wavelets, consistent with development of thyro-hyoid muscle fatigue. The results of this study identified fatigue as the main factor leading to exercise induced palatal instability and DDSP in a group of racehorses. Further studies are required to evaluate the fiber type composition and metabolic characteristics of the thyro-hyoid muscles that could predispose to fatigue.