The emergence of repetitive transcranial magnetic stimulation (rTMS) as a relatively noninvasive probe of cortical function provides an opportunity to explore the relationships between regional brain activity and symptomatology across neuropsychiatric illnesses. In this article, we briefly review evidence from functional neuroimaging studies (principally those using positron emission tomography [PET] or single-photon emission computed tomography [SPECT]) and other studies suggesting regional brain involvement in anxiety disorders, specifically obsessive-compulsive disorder (OCD) and posttraumatic stress disorder (PTSD). We also review an initial controlled study conducted by our group using rTMS as a probe of prefrontal mechanisms in OCD. This discussion is not intended to be comprehensive, but rather to provide examples of disorders that, based on current knowledge, might be good candidates for the use of rTMS as a probe. In addition, we present case reports from pilot studies of rTMS in three patients with different primary anxiety disorder diagnoses, which illustrate some of the issues involved in such studies, as well as the effects observed. The possibility that rTMS may have therapeutic potential in anxiety disorders is also discussed.