The relationship between borderline personality disorder (BPD) and the affective disorders is controversial, and we have previously compared BPD and major depression (MD) with endocrinological measures and sleep electroencephalography (S-EEG). We have also compared BPD, MD and recurrent brief depression (RBD) using endocrine tests. We have proposed that depressive symptoms in BPD might have a biological substrate that is distinct from those in depressive illness without comorbid BPD. BPD has been proposed to overlap with RBD, which has been found to share perturbed biological substrates with MD, but we have not found the same biological pattern in BPD. When endocrinological data in BPD, MD and RBD were compared, we did not find evidence of biological linkage between BPD and RBD. To clarify the biological nature of depressive symptoms in BPD, we examined S-EEG characteristics in BPD, RBD, MD and controls. Among 20 BPD patients, 12 were also diagnosed as having clinical RBD. BPD patients showed differences in sleep continuity and especially in sleep architecture compared with RBD, MD and controls. BPD with or without clinical RBD did not show significant differences in any parameter. BPD with or without clinical RBD had less slow sleep activity not only than MD but also than non-borderline RBD patients. We propose that although BPD patients can have concomitant MD, they often exhibit a specific BPD-associated affective syndrome that is different from both MD and non-borderline RBD in the quality and duration of symptoms and the biological substrate.