The primary motor cortex (M1) is highly influenced by premotor/motor areas both within and across hemispheres. Dual site transcranial magnetic stimulation (dsTMS) has revealed interhemispheric interactions mainly at early latencies. Here, we used dsTMS to systematically investigate long-latency causal interactions between right-hemisphere motor areas and the left M1 (lM1). We stimulated lM1 using a suprathreshold test stimulus (TS) to elicit motor-evoked potentials (MEPs) in the right hand. Either a suprathreshold or a subthreshold conditioning stimulus (CS) was applied over the right M1 (rM1), the right ventral premotor cortex (rPMv), the right dorsal premotor cortex (rPMd) or the supplementary motor area (SMA) prior to the TS at various CS-TS inter-stimulus intervals (ISIs: 40–150 ms). The CS strongly affected lM1 excitability depending on ISI, CS site and intensity. Inhibitory effects were observed independently of CS intensity when conditioning PMv, rM1 and SMA at a 40-ms ISI, with larger effects after PMv conditioning. Inhibition was observed with suprathreshold PMv and rM1 conditioning at a 150-ms ISI, while site-specific, intensity-dependent facilitation was detected at an 80-ms ISI. Thus, long-latency interhemispheric interactions, likely reflecting indirect cortico-cortical/cortico-subcortical pathways, cannot be reduced to nonspecific activation across motor structures. Instead, they reflect intensity-dependent, connection- and time-specific mechanisms.