Previous studies in healthy volunteers reported a possible impact of high frequency repetitive transcranial magnetic stimulation (HF-rTMS) on stress hormones, like cortisol. In this sham-controlled, "single blind", crossover study, we examined whether HF-rTMS had an effect on the hypothalamic-pituitary-adrenal (HPA) axis, by analysing salivary cortisol levels. Two studies were conducted. First, HF-rTMS on the left dorsolateral prefrontal cortex (DLPFC) was performed in 28 young healthy female volunteers. Second, in a comparable, but different group of 26 healthy females, HF-rTMS was performed on the right DLPFC. Salivary cortisol levels were assessed before, immediately after and 30 min after real and sham HF-rTMS. We found no support for the hypothesis that one single session of HF-rTMS on the left or the right DLPFC has an immediate or delayed impact on the HPA-axis, as measured by salivary cortisol. Although we controlled for several methodological problems in HF-rTMS research, the hypothesis that one single session of HF-rTMS on the left or on the right DLPFC can influence the HPA-axis in healthy volunteers was not supported.