In the present study we tested the applicability of a paired-stimulus paradigm for the investigation of near-threshold (NT) stimulus processing in the somatosensory system using magnetoencephalography. Cortical processing of the NT stimuli was studied indirectly by investigating the impact of NT stimuli on the source activity of succeeding suprathreshold test stimuli. We hypothesized that cortical responses evoked by test stimuli are reduced due to the preactivation of the same finger representation by the preceding NT stimulus. We observed attenuation of the magnetic responses in the secondary somatosensory (SII) cortex, with stronger decreases for perceived than for missed NT stimuli. Our data suggest that processing in the primary somatosensory cortex including recovery lasts for <200 ms. Conversely, the occupancy of SII lasts ≥500 ms, which points to its role in temporal integration and conscious perception of sensory input.