The aim of the present study was to examine autonomic function in response to negatively and positively valenced pictures under different levels of conscious recognition. Heart period variability (HPV) and heart rate (HR) reactivity were studied in 53 males and females who were being shown pictures of angry and happy faces. The pictures, which were backwardly masked, were presented once every 30 s during a 5-min period and under three conditions (counterbalanced for type of facial expression): below the level of conscious recognition (17 ms), at an intermediate level (56 ms), and at a clearly recognizable level (2370 ms). Analyses of HR power spectrum (for 5 min in each condition) in the high frequency region (HF: 0.15-0.5 Hz) that reflects respiratory sinus arrhythmia, as well as analysis of phasic heart rate responses (7.5 s in 0.5 epochs following every picture presentation) were carried out. The main findings were that HF-power was higher, and cardiac midinterval acceleration lower, in response to angry as opposed to happy faces, a result obtained only for the men, however. No interaction effect between facial expression and the three exposure conditions was found, suggesting that the pictures induced emotional activation both subliminally and supraliminally. The results were discussed in terms of increased attention to aversive stimuli.