Facial micro-expressions are facial expressions expressed briefly (less than 500 ms) and involuntarily. Described only in humans, we investigated whether micro-expressions could also be expressed by non-human animal species. Using the Equine Facial action coding system (EquiFACS), an objective tool based on facial muscles actions, we demonstrated that a non-human species,Equus caballus, is expressing facial micro-expressions in a social context. The AU17, AD38 and AD1 were selectively modulated as micro-expression—but not as standard facial expression (all durations included)—in presence of a human experimenter. As standard facial expressions, they have been associated with pain or stress but our results didn’t support this association for micro-expressions which may convey other information. Like in humans, neural mechanisms underlying the exhibit of micro-expressions may differ from those of standard facial expressions. We found that some micro-expressions could be related to attention and involved in the multisensory processing of the ‘fixed attention’ observed in horses’ high attentional state. The micro-expressions could be used by horses as social information in an interspecies relationship. We hypothesize that facial micro-expressions could be a window on transient internal states of the animal and may provide subtle and discreet social signals.