The aim of the study was to set up assessment indicators for early elimination of horses that are not trainable or low efficient for training by comparing difference of behavioral response and heart rate on stimulation of desensitization training in horses. The animals used in this study were 8 untrained cross-bred horses (Thoroughbred and Jeju-horse) in Jeju island. Changes of heart rates and behavioral response of each horses were compared before and after desensitization training using a plastic bag on its tip. The result showed that the horses with their severe behavioral response were also high in heart rate during early stage of desensitization training, and the increased heart rates were recovered back to the base level according to the process of the training. The horses that quickly recovered in heart rate also showed same tendency in behavioral response. The horses that their recovery in heart rate and behavioral response in early stage of the desensitization training were late, showed insufficient results of the additional desensitization training. We conclude that assessment of heart rate and behavioral response in the early stage of desensitization training could be used as indicators to predict the effectiveness of desensitization or other kinds of training in horses.