Horses have the ability to generate a remarkable repertoire of facial expressions, some which have been linked to certain emotional states, for example pain. Studies suggest that facial expressions may be a more ‘honest’ expression of emotional state in horses than behavioral or physiological parameters. This study sought to describe the facial expressions during stress of healthy horses free of pain, using a standardized method of recording facial expressions in video. Stress was induced in 28 horses by subjecting them to road transport and 10 of these horses were also subjected to social isolation. The horses served as their own control. A body-mounted, remote controlled heart rate monitor provided continuous heart rate measurements during the interventions. The horses’ facial expressions were video-recorded during the interventions. Frequency and duration of each facial expression were then determined, according to the Equine Facial Action Coding System. Heart rate increased during the stressful interventions (p=0.01), confirming that the interventions were stressful. Using both the human investigation- and the co-occurrence methods, the following facial traits could be observed during stress: eye white increase (p<0.001), nostril dilator (p<0.001), upper eyelid raiser (p<0.001), inner brow raiser (p=0.042), tongue show (p<0.001) along with an increase in ‘ear flicker’ (p<0.001) and blink frequency (p<0.001). The facial actions were successfully used to train a machine-learning classifier to discriminate between stressed and calm horses, with an accuracy of 74.2 %. Most of the facial features identified correspond well with previous research on the subject, for example flared nostrils, repetitive mouth behaviors, increased eye white, tongue show and ear movements. Some features selected as indicative of emotional pain-free stress are used in face-based pain assessment tools, such as dilated nostrils, eye white increase or inner brow raiser. The relation between facial expressions of stress and pain should therefore further be studied.