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Frequency-domain indices of heart rate variability (HRV) have been used as markers of sympathovagal balance. However, they have been shown to be degraded by interindividual or task-dependent variability, and especially variations in breathing frequency. The study introduces a method to analyze respiration-(vagally) mediated HRV, to better assess subtle variations in sympathovagal balance using ECG recordings. The method enhances HRV analysis by focusing the quantification of respiratory sinus arrhythmia (RSA) gain on the respiratory frequency. To this end, instantaneous respiratory frequency was obtained with ECG-derived respiration (EDR) and was used for variable frequency complex demodulation (VFCDM) of R-R intervals to extract RSA. The ability to detect cognitive stress in 27 subjects (athletes and nonathletes) was taken as a quality criterion to compare our method to other HRV analyses: Root mean square of successive differences, Fourier transform, wavelet transform, and scaling exponent. Three computer-based tasks from MATB-II were used to induce cognitive stress. Sympathovagal index (HF nu ) computed with our method better discriminates cognitive tasks from baseline, as indicated by P values and receiver operating characteristic curves. Here, transient decreases in respiratory frequency have shown to bias classical HRV indices, while only EDR-VFCDM consistently exhibits the expected decrease in the HF nu index with cognitive stress in both groups and all cognitive tasks. We conclude that EDR-VFCDM is robust against atypical respiratory profiles, which seems relevant to assess variations in mental demand. Given the variety of individual respiratory profiles reported especially in highly trained athletes and patients with chronic respiratory conditions, EDR-VFCDM could better perform in a wide range of applications.