Recent evidence suggests that the motor system undergoes very specific modulation in its functional state during the different sleep stages. Here we test the hypothesis that changes in the functional organization of the motor system involve both cortical and subcortical levels and that these distributed changes are interrelated in defined frequency bands. To this end we evaluated functional connectivity between motor and non-motor cortical sites (fronto-central, parieto-occipital) and the globus pallidus (GP) in human non-REM sleep in seven patients undergoing deep brain stimulation (DBS) for dystonia using a variety of spectral measures (power, coherence, partial coherence and directed transfer function (DTF)). We found significant coherence between GP and fronto-central cortex as well as between GP and parieto-occipital cortex in circumscribed frequency bands that correlated with sleep specific oscillations in 'light sleep' (N2) and 'slow-wave sleep' (N3). These sleep specific oscillations were also reflected in significant coherence between the two cortical sites corroborating previous studies. Importantly, we found two different physiological activities represented within the broad band of significant coherence between 9.5 and 17 Hz. One component occurred in the frequency range of sleep spindles (12.5-17 Hz) and was maximal in the coherence between fronto-central and parieto-occipital cortex as well as between GP and both cortical sites during N2. This component was still present between fronto-central and parieto-occipital cortex in N3. Functional connectivity in this frequency band may be due to a common input to both GP and cortex. The second component consisted of a spectral peak over 9.5-12.5 Hz. Coherence was elevated in this band for all topographical constellations in both N2 and N3, but especially between GP and fronto-central cortex. The DTF suggested that the 9.5-12.5 Hz activity consisted of a preferential drive from GP to the fronto-central cortex in N2, whereas in N3 the DTF between GP and fronto-central cortex was symmetrical. Partial coherence supported distinctive patterns for the 9.5-12.5 and 12.5 and 17 Hz component, so that only coherence in the 9.5-12.5 Hz band was reduced when the effects of GP were removed from the coherence between the two cortical sites. The data suggest that activities in the GP and fronto-central cortex are functionally connected over 9.5-12.5 Hz, possibly as a specific signature of the motor system in human non-REM sleep. This finding is pertinent to the longstanding debate about the nature of alpha-delta sleep as a physiological or pathological feature of non-REM sleep.