Background Understanding how different brain regions interact with one another is at the heart of current endeavors in cognitive and basic neuroscience. Unlike most neuroimaging techniques, transcranial magnetic stimulation (TMS) allows the establishment of causal relationships in the study of the functional architecture of the human brain. While this tool is increasingly used to probe the functional and causal nature of the associations between brain regions, a comprehensive guide documenting the various existing stimulation protocols is currently lacking, limiting its use. Objective The main objective of the current work is to characterize the various dual-coil TMS protocols used to probe effective connectivity and plasticity within the motor system. In addition, we want to propose a short TMS battery that could be used in clinical and research settings. Method Articles using dual-coil TMS indexed in PubMed and Medline published between 1990 and 2015 were included in the review. Results A wide range of stimulation parameters has been used to probe connectivity and plasticity. However, a few protocols have been shown to produce robust effects, mostly inhibitory in nature. Conclusion Dual-coil TMS offers the distinctive opportunity to investigate effective connectivity and plasticity between different parts of the brain. Sites of stimulation, stimulation intensity, inter-stimulus interval and coil orientation are crucial factors to consider when using this technique. We propose a brief battery of tests that could be used to assess effective brain connectivity in clinical populations.