Electroencephalography (EEG) spikes and focal epileptic seizures are generated in circumscribed cerebral networks that have been insufficiently described. For precise time and spatial domain network characterization, we applied in patients with focal epilepsy dense array 256-channel EEG recordings with causal connectivity estimation by using time-resolved partial directed coherence and 3T-magnetic resonance imaging-derived cortical and thalamus integrity reconstruction. Before spike generation, significant theta and alpha bands driven information flows alterations were noted from both temporal and frontal lobes to the thalamus and from the thalamus to the frontal lobe. Medial dorsal and ventral anterior nuclei of the thalamus were delimited as possible pacemakers. Markedly reduced thalamic volumes and impaired cortical integrity in widespread areas predicted the altered information flows. Our data reveal distinct patterns of connectivity involving the thalamus and frontal cortex that are both directly and causally involved in spike generation. These structures might play an essential role in epileptogenesis and could be targeted in future therapeutic approaches.