In order to investigate the effects of short road transport stress on total and free iodothyronines, body weight (BW), rectal temperature and heart rate (HR) changes, 126 healthy stallions were studied in basal conditions, before and after transport. A total of 60 Thoroughbred and 66 crossbred stallions aged 4 to 15 years with previous travelling experience were transported by road in a commercial trailer for a period of about 3 to 4 h (distance under 300 km). Blood samples and functional variables were collected in each horse box, one week before loading and transport in basal conditions (control samples), one week later immediately before loading (pre-samples) and again after transport and unloading (about 3 to 4 h) in each new horse box, within 30 min of their arrival at the breeding stations (post-samples). Compared to the before-transport values, increases in circulating T3, T4 and fT4 levels (P < 0.01) were observed after transport, irrespective of breed, but not for fT3 levels. Lower T4 and fT4 levels were observed in basal II (at 1100 h) (P < 0.01) than in basal I (at 0800 h) conditions and before transport. Thoroughbreds showed higher fT3 (P < 0.05) and fT4 (P < 0.01) levels after transport than crossbred stallions. No significant differences were observed for T3 and T4. Compared to the before-transport values, significant increases in rectal temperature (P < 0.01) and HR (P < 0.05) were observed after transport. No differences were observed between basal I, II and before values for functional variables. Significant correlations between T3 and rectal temperature, BW and HR were found. The results indicate that short road transport induces a preferential release of T3, T4 and fT4 hormones from the thyroid gland in relation to different breed, and an increase in rectal temperature and HR. No significant changes in BW were observed. No differences were observed in relation to different ages. The data obtained suggest that the stallion’s thyroid hormones and functional variables may play an important role in assessing the effects of transport stress and a horse’s coping strategy.