Commonly used noninvasive fetal monitoring is based on fetal heart rate (FHR) variability analysis of the Doppler ultrasound signal coming from the mechanical activity of the fetal heart. However, in most of bedside monitors there is an invasive option that during a labor the FHR signal can be obtained directly from the scalp electrode. The determination of cardiac intervals using the Doppler ultrasound signal is more difficult than in electrocardiography, where the R-waves are evident. We investigated the influence of the signal acquisition methods on the FHR variability analysis. The LabView based instrumentation for simultaneous signal acquisition from two fetal monitor channels recording mechanical and electrical heart activity was developed. The 185 pairs of indices describ-ing both the long- and the short-term FHR variability were calculated within one-minute windows. The results reveal that the accuracy of the ultrasound method is to low for reliable measurement of beat-to-beat intervals, what is particularly visible in the reduction of the short-term variability indices.