Heart rate variability (HRV) has been widely used as a measure of vagal activation in physiological, psychological and clinical examinations. We studied the within-subject quantitative relationship between HRV and vagal effects on the heart in different body postures during a gradually decreasing vagal blockade. Electrocardiogram and respiratory frequency were measured in 8 endurance athletes and 10 participants of non-endurance sports in supine, sitting and standing postures prior to the blockade, under vagal blockade (atropine sulfate 0.04 mg/kg) and four times during a 150-min recovery from the blockade. Fast Fourier transform was used to calculate low frequency power (LFP, 0.04-0.15 Hz), high frequency power (HFP, 0.15-0.40 Hz) and total power (TP, 0.04-0.40 Hz). A within-subject linear regression analysis of recovery time on each HRV index was conducted. Complete vagal blockade decreased all HRV significantly, particularly HFP (p < 0.001). A linear fit explained a large portion of the within-subject variance between recovery time and natural log-transformed (ln) HRV indices in every posture, with coefficients of determination (R²) in the supine posture (mean±SD): 98±2% for mean R-R interval, 87±10% for lnLFP, 87±13% for lnHFP and 91±10% for lnTP. Neither body posture nor endurance training background had an impact on R²s. There was marked between-subject variation in the R²s, slopes and intercepts. In conclusion, all HRV, particularly HFP, is predominantly under vagal control. Within subjects, lnLFP, lnHFP and lnTP increased linearly with the gradually decreasing vagal blockade in all postures.