The role of the primary somatosensory cortex in thermal pain perception has been established. However, the cortical circuitry that mediates the thermo-nociceptive information processing has not been elucidated. The aim of present study was to investigate the intracortical synaptic currents in primary somatosensory cortex evoked by short laser pulses and to determine their transmission pathway. Noxious CO2 laser pulse stimuli or innocuous electrical and mechanical stimuli were delivered to the hind paw of halothane-anesthetized rats. Multi-channel field potentials were recorded simultaneously in primary somatosensory cortex and laminar-specific transmembrane currents were analyzed using a current source density method. A distinct spatial-temporal pattern of intra-cortical sink source currents was evoked by laser pulse stimuli. The amplitude of the early component was graded by laser energy output and influenced by contralateral signals, whereas the late components were not intensity-dependent and exhibited bilateral excitation. Intra-cortical current flows revealed that synaptic activation occurred initially at layers IV and VI separately and then was relayed transynaptically to the more superficial and the deeper layers. Latency, amplitude and intracortical distributions of the activated intra-cortical currents evoked by noxious stimuli differed significantly from those evoked by innocuous stimuli. Conduction velocity data together with the results of tetrodotoxin, capsaicin and morphine treatments indicated that the early and late components were mediated separately by A-delta and C fibers. Our results suggest that large and small diameter thermal nociceptive afferents generated laminar-specific intracortical synaptic currents in primary somatosensory cortex and that these excitatory synaptic currents were conveyed separately by lateral and medial thalamic nuclei.