Transcallosal connectivity between the hand areas of the two primary motor cortices (M1) is important for coordination of unimanual and bimanual hand motor function. Effective connectivity of this M1-M1 pathway can be tested in the form of short-interval interhemispheric inhibition (SIHI) using dual-coil transcranial magnetic stimulation (TMS). Recently, we and others have demonstrated that the phase of the ongoing sensorimotor -rhythm has significant impact on corticospinal excitability as measured by motor evoked potential (MEP) amplitude, and repetitive TMS of the high-excitability state (trough of the -rhythm) but not other states resulted in long-term potentiation-like MEP increase. Here, we tested to what extent the phase of the ongoing -rhythm in the two M1 cortices affects long-term change in SIHI. In healthy subjects we applied cortico-cortical paired associative stimulation (ccPAS) in four different -phase conditions in the left conditioning M1 and right test M1 (trough-trough, trough-positive peak, positive peak-trough, random phase). We found long-term strengthening of SIHI but no differential effect of phase conditions. Findings point to a distinct regulation of plasticity of corticospinal vs. M1-M1 connectivity. The observed ccPAS-induced strengthening of effective M1-M1 connectivity (SIHI) may be utilized for therapeutic applications that potentially benefit from modification of interhemispheric excitation/inhibition balance.