Limited information exists about changes in circulating thyroid hormone concentrations during prolonged endurance exercise in horses. To examine the effects of prolonged exercise on serum iodothyronine concentrations in horses performing endurance exercise of varying distances. Serum concentrations of iodothyronines were measured in horses before and after completion of 40, 56, 80 and 160 km endurance rides (Study 1); daily during a 5 day, 424 km endurance ride (Study 2); and before and for 72 h after completion of a treadmill exercise test simulating a 60 km endurance ride (Study 3). In Study 1, 40 and 56 km of endurance exercise had little effect on serum iodothyronine concentrations with the exception of a 10% decrease (P<0.05) in free thyroxine (FT4) concentration after the 56 km ride. In contrast, total thyroxine (T4), total triiodothyronine (T3), FT4 and free triiodothyronine (FT3) concentrations all decreased (P<0.05) after successful completion of 80 and 160 km rides, with decreases ranging from 13-31% and 47-54% for distances of 80 and 160 km, respectively. Further, pre-ride T4 concentration was lower (P<0.05) and FT3 concentration was higher (P<0.05) in horses competing 160 km as compared to horses competing over shorter distances. In Study 2, serum concentrations of T4, T3 and reverse triiodothyronine (rT3) progressively decreased (P<0.05) over the course of the multi-day ride. In Study 3, the greatest decrease (P<0.05) in all iodothyronines was observed at 12 h of recovery, ranging from 25% for FT4 to 53% for FT3, but all thyroid hormone concentrations had returned to the pre-exercise values by 24 h of recovery. Endurance exercise results in transient decreases in serum iodothyronine concentrations. These data are important to consider when thyroid gland function is assessed by measurement of serum iodothyronine concentrations in endurance horses.