Repetitive transcranial magnetic stimulation (rTMS) has been found to ameliorate symptoms in major depression. However, its mechanism of action has to be further elucidated and the relationship between responses to rTMS and other antidepressant interventions except electroconvulsive therapy has not been investigated to date. Here we studied in an open trial whether the response to partial sleep deprivation may predict the clinical outcome of rTMS treatment. Thirty-three drug-free patients suffering from a major depressive episode underwent a partial sleep deprivation at least 5 days prior to rTMS and subsequently received 10 sessions of 10 Hz rTMS of the left prefrontal cortex. After rTMS a significant overall improvement of 32% on the Hamilton Rating Scale for Depression was observed. Forty-two percent of patients showed an antidepressant response after rTMS. Amelioration of depression after partial sleep deprivation was inversely correlated with improvement after rTMS. There was no clinically applicable predictive value of the response to partial sleep deprivation for the outcome after rTMS. Apparently, different subgroups of depressed patients respond to both interventions. Further studies are needed to characterize the response to rTMS by means of clinical and biological parameters.