The aim of this experiment was to explore changes in the vagally mediated heart rate variability (HRV) of flight phobics during exposure to feared stimuli. A paced breathing task was included to control for respiration effects. Sixty-one flight phobics (40 women) with a mean age of 39.07 years (SD = 11.24) participated in the study. The root mean of the squared successive interbeat intervals differences (RMSSD) was taken as the time domain measure of HRV. High frequency (HF: 0.15-0.4 Hz) and low frequency (LF: 0.04-0.15 Hz) band power was calculated on the ECG recordings obtained during free breathing baseline (BL), paced breathing (PB), and exposure (E) to fearful stimuli. Heart rate unexpectedly increased from BL to PB, and decreased from PB to E, while no differences were found between BL and E. No changes in the RMSSD were seen across conditions. HF band power increased, as expected, from BL to PB, and a significant decrease was found from PB to E. LF band power, as well as the LF/HF ratio, increased from BL to E. Discussion focuses on (a) the role of the parasympathetic and the sympathetic nervous systems in fear-related situations, and (b) the effects of paced breathing in preparing the system to cope with threat.