INTRODUCTION: Coincidental stimulation of the sympathetic and parasympathetic nervous system can cause "autonomic conflict" and consequent cardiac arrhythmias. The present study tested the hypotheses that: 1) cardiac arrhythmias would be seen in those undertaking helicopter underwater escape training (HUET); 2) the occurrence of arrhythmias in individuals could be predicted; and 3) the heart rate response to HUET would habituate with repeated runs. METHODS: There were 26 male volunteers who each undertook 5 HUET submersions into water at 29.5 degrees C, with each run separated by 10 min. Each submersion included a 3-min, 40-s pre-submersion period, a 10-s submersion, and 40-s post-submersion period. Participants wore a three-lead telemetric ECG system beneath an immersion suit and underclothing. Skin temperature was measured in one participant. Each participant undertook tests to establish their autonomic function, including heart rate variability, face immersion, cold pressor test, and aerobic capacity assessment. RESULTS: The heart rate response to HUET was reduced by the fourth run when compared to the first run. Across all runs, 32 cardiac arrhythmias were identified (25%) in 22 different participants; all but 6 of the arrhythmias occurred just after submersion. Only aerobic fitness appeared inversely associated with the occurrence of arrhythmias. CONCLUSIONS: The heart rate response to HUET habituates. HUET produces cardiac arrhythmias; these are asymptomatic and probably of little clinical significance in young, fit individuals. It remains to be seen if this is the case with either an older, less fit cohort of people or in those undertaking longer breath holds in colder water.