Paired associative stimulation (PAS) repeatedly pairs electrical nerve stimulation with transcranial magnetic stimulation of the contralateral motor hand area (M1(HAND)). Depending on the interstimulus interval, PAS can induce a long-term potentiation (LTP)-like facilitation or long-term depression (LTD)-like suppression of cortical excitability. In three experimental sessions, 12 awake men received PAS of the right median nerve and left M1(HAND) in the evening before sleep. To optimize the timing of paired stimulation in M1(HAND), the interstimulus interval of PAS was adjusted to the individual N20-latency of the somatosensory evoked potential to induce LTP-like effects (PAS(N20+2ms)), LTD-like effects (PAS(N20-5ms)), or no timing-dependent after-effects (PAS(control)). Motor-evoked potentials (MEPs) showed high interindividual variations in the conditioning effects of PAS(N20+2ms) and PAS(N20-5ms) on cortical excitability. However, PAS(control) allowed us to adjust for any unspecific stimulation effects and the MEP increase after PAS(N20+2ms) differed significantly from the MEP decrease after PAS(N20-5ms). PAS(N20+2ms) and PAS(N20-5ms) also had a differential effect on regional expression of slow waves and slow spindle activity during the first hour of subsequent non-rapid eye movement (NREM) sleep. At the electrode sites overlying the conditioned M1(HAND) and the adjacent premotor cortex, local expression of slow spindle activity was significantly correlated with interindividual differences in the efficacy of PAS(N20+2ms) and PAS(N20-5ms) to potentiate or suppress cortical excitability. This correlation indicates that PAS shapes the local regulation of slow sleep spindles during subsequent NREM sleep.