Transcranial magnetic stimulation (TMS) is a safe and easy technique for stimulating neurons in the human central nervous system. Studies combining TMS with drugs in healthy subjects and patients have advanced our knowledge of how TMS activates brain circuits and led to new techniques for evaluating the function of specific systems. For example, TMS techniques can detect effects on axon membranes, glutamatergic and GABAergic synapses and the influence of catecholaminergic systems, as well as group differences due to genetic variations in the response to drugs. With this knowledge base, TMS can now be used to explore and compare the effects of drugs on brain systems and may also serve as a surrogate for behavioral responses in clinical trials.