The application of transcranial magnetic stimulation (TMS) to investigate important questions in cognitive neuroscience has increased considerably in the last few years. TMS can provide substantial insights into the nature and the chronometry of the computations performed by specific cortical areas during various aspects of cognition. However, the use of TMS in cognitive studies has many potential perils and pitfalls. Although TMS can help bridge the gap between psychological models and brain-based arguments of cognitive functions, hypothesis-driven carefully designed experiments that acknowledge the current limitations of TMS are critical.