Emotion-modulated startle is a robust phenomenon that has been demonstrated in a wide range of experimental situations. Similarly, heart rate variability (HRV) has been associated with a diverse range of processes including affective and attentional regulation. The present study sought to examine the relationship between these two important measures of affective behavior. Ninety female participants viewed pleasant, neutral, and unpleasant pictures while exposed to acoustic startle stimuli. The eyeblink startle was recorded both during the affective foregrounds and during intertrial intervals. HRV was assessed during a resting baseline and relationships between HRV and startle magnitudes examined. Results indicated that resting HRV was inversely related to startle magnitude during both intertrial intervals and affective foregrounds. In addition, the participants with the highest HRV showed the most differentiated emotion-modulated startle effects, whereas those with the lowest HRV, compared to those with the highest HRV, showed significantly potentiated startle to neutral foregrounds and marginally potentiated startle to pleasant foregrounds. The findings are consistent with models that posit that prefrontal cortical activity modulates subcortical motivation circuits. These results have important implications for the use of startle probe methodology and for HRV in the study of emotional regulation and dysregulation.