Heart rate variability (HRV) reflects cardiac and autonomic nervous system activity. It is usually measured over a relatively prolonged period and presented using multiple parameters. Here, we studied rapid HRV changes during airway obstruction using a short (1 min) sampling window. Forty healthy volunteers underwent a trial of obstructed breathing. Heart rate was recorded during three consecutive sets comprised of 1-min control followed by 1 min of obstructed breathing, with 1 min of rest between sets. Time and frequency domain analysis were used to compare HRV during control versus obstructed breathing. Compared with control, HRV intensely increased during obstructed breathing: R-R intervals (time between consecutive R waves) standard deviation increased from 65 to 108 msec (P < 0.0001), root mean square of successive R-R interval from 61 to 82 msec (P = 0.001), number of pairs of successive R-R intervals that differ by more than 50 msec (NN50) from 16.5 to 25.3 events (P < 0.0001), and proportion of NN50 divided by total number of R-R intervals from 26.6 to 35.1% (P = 0.001). Low frequency power increased by more than fourfold (P < 0.0001), allowing 90% sensitivity and 75% specificity for identifying airway obstruction (ROC area 0.88, P < 0.0001). We observed a rapid intense increase in HRV during obstructed breathing, significant enough to detect during a short 1-min sampling window. These findings suggest that HRV may be useful for rapid detection of airway obstruction, especially in situations where end-tidal CO(2) monitoring is not optimal, such as during partial airway obstruction.