Electromechanical coupling of the fetal heart can be evaluated using the intervals between the onset of the QRS complex of the fetal electrocardiogram (fECG) and opening and closing of the cardiac valves. An automated method was proposed in our previous study to estimate these intervals from Doppler Ultrasound (DUS) signal and fECG for normal fetuses. In the current study this method was applied to the fetuses with heart anomalies to investigate the effect of anomalies on fetal cardiac intervals. Results show that the Pre-ejection period (PEP) and Isovolumetric Contraction Time (ICT) were affected by the anomalies. They were both shortened for three out of four anomalies and lengthened for one heart anomaly case. Results will be a background for a further study on more heart anomaly cases to develop a reliable marker for early diagnosis.