Introduction Studies on fear conditioning have made important contributions to the understanding of affective learning mechanisms as well as its applications (e.g., anxiety disorders, post-traumatic stress disorder). However, central mechanisms of sleep related consolidation of fear memory in humans have been almost neglected by previous studies. Objectives In the current study we aimed to test effects of sleep and a period wakefulness on fear conditioned responses. Methods In our experiment in a group 18 healthy volunteers event-related brain potentials (ERP), heart rate variability (HRV) and behavioral responses were recorded during a fear conditioning procedure presented twice, before daytime sleep (2h) or control intervention (a period of wakefulness) and after. The conditioning procedure involved pairing of a neutral tone (CS+) with a highly unpleasant sound (UCS+). Results Differential conditioning manifested itself in the contingent negative variance (CNV)-like slow ERP component. Both period of sleep and wakefulness resulted in an increased amplitude of the CNV to CS+. But we did not find an interaction effect of Time (Pre-Post) by Intervention (Sleep-Wake), suggesting that sleep did not affect the conditioned response differently as compared to a period of wakefulness. An apparent increase in HRV after a period of wakefulness did not affect fear conditioned responses (CNV and valence ratings). Conclusions To summarize, the data indicate that fear memories are consolidated with the course of time with no beneficial effect of sleep; relearning of fear causes stronger differential responses as measured by slow wave amplitude but not behavior; increase of HRV does not affect fear learning.