Noninvasive brain stimulation is a valuable investigative tool and has potential therapeutic applications in cognitive neuroscience, neurophysiology, psychiatry, and neurology. Transcranial magnetic stimulation (TMS) is particularly useful to establish and map causal brain-behavior relations in motor and nonmotor cortical areas. Neuronavigated TMS is able to provide precise information related to the individual's functional anatomy that can be visualized and used during surgical interventions and critically aid in presurgical planning, reducing the need for riskier and more cumbersome intraoperative or invasive mapping procedures. This article reviews methodological aspects, clinical applications, and future directions of TMS-based mapping.