A three-stage methodology for the extraction of maternal and fetal heart rate using abdominal ECG leads, is presented. In the first stage, the maternal R-peaks and fiducial points (maternal QRS onset and offset) are detected, using multiscale principal components analysis (MSPCA) and the Smoothed Nonlinear Energy Operator (SNEO). Maternal fiducial points are used to eliminate the maternal QRS complexes from the abdominal ECG recordings. In the second stage, again MSPCA and SNEO are employed in order to detect the fetal heart beats that do not overlap with the maternal QRSs (eliminated from the first stage). The extraction of the fetal heart rate is accomplished in the last stage, using a histogram based technique in order to identify the positions of the fetal heart beats that overlap with the maternal QRSs. Real signals, recorded from different pregnant women and different weeks of gestation, are used for the evaluation of the proposed methodology and the obtained results indicate high performance (accuracy 95%).