BACKGROUND: Transcranial Magnetic Stimulation (TMS) is effective in major depressive episodes (MDE). However, MDE may follow a chronic, relapsing course, and some individuals may not satisfactorily respond to a first course of TMS. OBJECTIVE: To investigate the outcome of second courses of TMS. METHOD: A naturalistic investigation-we prospectively studied 30 MDE in-patients and routinely collected information, including pre- and post-treatment with Six-item Hamilton Depression Rating Scale (HAMD6), a six-item Visual Analogue Scale (VAS6) and the Clinical Global Impression-Severity (CGI-S). Two categories of patients were considered: i) those who had remitted with a first course, but relapsed, and ii) those who had not remitted with the first course. RESULTS: Thirty individuals received a second TMS course. The mean time to the second course was 27.5 weeks. Based on the HAMD6, 26 (87%) achieved remission after the first course, and 22 (73%) achieved remission after the second course. Furthermore, based on the HAMD6 results, of the four patients who did not achieve remission with a first course, three (75%) did so with a second course. CONCLUSION: In MDE, a second course of TMS is likely to help those who remitted to a first course and then relapsed, as well as those who did not achieve remission with a first course.