In the present study a computer-assisted exposure-based treatment was applied to 54 flight phobics and the predictive role of vagally mediated heart rate (HR) variability (high frequency, 0.15-0.4 Hz band power) and heart rate entropy (HR time series sample entropy) on treatment outcome was investigated. Both physiological measures were taken under controlled breathing at 0.2 Hz and during exposure to a fearful sequence of audiovisual stimuli. Hierarchical regression analyses were conducted to assess the predictive power of these variables in these conditions on treatment self-report measures at the end of treatment and at 6 months follow-up, as well as on the behavioral treatment outcome (i.e. flying at the end of treatment). Regression models predicting significant amounts of outcome variance could be built only when HR entropy was added to the HR variability measure in a second step of the regression analyses. HR variability alone was not found to be a good predictor of neither self-reported nor behavioral treatment outcomes.