Spontaneous BRS estimates may considerable vary according to the technique of blood pressure and heart rate assessment. To optimise and standardise BRS estimation for clinical use we evaluated possible differences between spontaneous BRS indices estimated from either finger plethysmography or radial tonometry. Forty-five healthy volunteers underwent simultaneous recordings of electrocardiogram, finger plethysmography and radial tonometry in supine position and during 60° head-up tilt. BRS was computed by spectral analysis from either R–R time series and/or arterial pressure pulse. Radial tonometry generated higher mean BRS estimates than finger plethysmography. The difference decreased upon postural change from supine to upright. In the upright position, BRS estimates based on R–R interval proved to be generally lower compared to BRS indices estimated from arterial pressure pulse. The ratio of low-to-high-frequency power of inter-systolic interval and systolic blood pressure from tonometry was lower than that from plethysmography in supine and approximated in upright position. Spectral parameters of inter-systolic interval and R–R interval did not differ in supine but diverged in upright position. Changes of spectral parameters were most pronounced in R–R interval. Arterial pressure pulse is adequate for estimation of BRS under resting conditions but it may distort BRS estimates under physical load. We, therefore, recommend using an ECG signal for BRS estimation especially in non-stationary conditions.