Empathy is a multifaceted phenomenon that is difficult to measure. Self-report questionnaires are the most common and well-validated measures while currently no validated protein biomarkers associated with the empathic reaction have been established. Trigger films have been previously used in psychological research to evoke emotions. Thus, in the present randomized cross-over study we investigated the responses of nine salivary biomarkers that have been related to emotions and stress following an empathy triggering and a control film sequence. Additionally, questionnaires for empathy (Saarbrucken Personality Questionnaire (SPQ)) and current mental stress were applied and participants were asked to assess the film protagonists’ emotions using the Positive and Negative Affect Schedule. Data from 46 participants were included in the analysis. α-Amylase, IgA, IL-1β and estradiol showed a significantly different response between the empathy and control intervention. Moreover, normalized levels of these biomarkers significantly correlated with single scales of the SPQ (control film sequence: α-amylase and IgA with personal distress; estradiol with empathic concern; IL-1β with fantasy; empathy triggering film sequence: IgA with empathic concern, fantasy and the total empathy score). These findings indicated that the observed changes in salivary biomarker levels were reflective of a physiological response to the empathy triggering film sequence. Future studies using different triggers and settings will show if the identified biomarkers can be considered as surrogate markers for empathic reactions in general.