AbstractWe propose a novel cerebral source extraction method (functional source separation, FSS) starting from extra‐cephalic magnetoencephalographic (MEG) signals in humans. It is obtained by adding a functional constraint to the cost function of a basic independent component analysis (ICA) model, defined according to the specific experiment under study, and removing the orthogonality constraint, (i.e., in a single‐unit approach, skipping decorrelation of each new component from the subspace generated by the components already found). Source activity was obtained all along processing of a simple separate sensory stimulation of thumb, little finger, and median nerve. Being the sources obtained one by one in each stage applying different criteria, the a posteriori “interesting sources selection” step is avoided. The obtained solutions were in agreement with the homuncular organization in all subjects, neurophysiologically reacting properly and with negligible residual activity. On this basis, the separated sources were interpreted as satisfactorily describing highly superimposed and interconnected neural networks devoted to cortical finger representation. The proposed procedure significantly improves the quality of the extraction with respect to a standard BSS algorithm. Moreover, it is very flexible in including different functional constraints, providing a promising tool to identify neuronal networks in very general cerebral processing. Hum Brain Mapp, 2006. © 2006 Wiley‐Liss, Inc.