Patients with borderline personality disorder (BPD) exhibit impairment in labeling of facial emotional expressions. However, it is not clear whether these deficits affect the whole domain of basic emotions, are valence-specific, or specific to individual emotions. Whether BPD patients' errors in a facial emotion recognition task create a specific pattern also remains to be elucidated. Our study tested two hypotheses: first, we hypothesized, that the emotion perception impairment in borderline personality disorder is specific to the negative emotion domain. Second, we hypothesized, that BPD patients would show error patterns in a facial emotion recognition task more commonly and more systematically than healthy comparison subjects. Participants comprised 33 inpatients with BPD and 32 matched healthy control subjects who performed a computerized version of the Ekman 60 Faces test. The indices of emotion recognition and the direction of errors were processed in separate analyses. Clinical symptoms and personality functioning were assessed using the Symptom Checklist-90-Revised and the Young Schema Questionnaire Long Form. Results showed that patients with BPD were less accurate than control participants in emotion recognition, in particular, in the discrimination of negative emotions, while they were not impaired in the recognition of happy facial expressions. In addition, patients over-attributed disgust and surprise and under-attributed fear to the facial expressions relative to controls. These findings suggest the importance of carefully considering error patterns, besides measuring recognition accuracy, especially among emotions with negative affective valence, when assessing facial affect recognition in BPD.