Technological development aims at fetal monitoring during pregnancy using the noninvasive fetal electrocardiogram (ECG). However, the noninvasive fetal ECG recorded from the mother’s abdomen is contaminated with several noise sources among which the maternal ECG is the most prominent. In the present study, the problem of noninvasive fetal ECG extraction is tackled using multi-modality. In the multi-modal concept, beside ECG signal, this approach benefits from the phonocardiogram (PCG) signal as another signal modality, which can provide complementary information about the fetal ECG. Multi-modality is based on the Gaussian process modeling, in this study, in order to provide the possibility of flexible models and nonlinear estimations.