Cognitive functions involve not only cortical but also subcortical structures. Subcortical sources, however, contribute very little to magnetoencephalographic (MEG) and electroencephalographic (EEG) signals because they are far from external sensors and their neural architectonic organization often makes them electromagnetically silent. Estimating the activity of deep sources from MEG and EEG (M/EEG) data is thus a challenging issue. Here, we review the influence of geometric parameters (location/orientation) on M/EEG signals produced by the main deep brain structures (amygdalo-hippocampal complex, thalamus and some basal ganglia). We then discuss several methods that have been utilized to solve the issues and localize or quantify the M/EEG contribution from deep neural currents. These methods rely on realistic forward models of subcortical regions or on introducing strong dynamical priors on inverse solutions that are based on biologically plausible neural models, such as those used in dynamic causal modeling (DCM) for M/EEG.