Objectives The therapeutic effects of Transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS) in patients with major depression have shown promising results; however, there is a lack of mechanistic studies using biological markers (BM) as an outcome. Therefore, our aim was to review non-invasive brain stimulation trials in depression using BM. Method The following databases were used for our systematic review: MEDLINE, Web of Science, Cochrane, and SCIELO. We examined articles published before November 2012 that used TMS and tDCS as an intervention for depression and had BM as an outcome measure. The search was limited to human studies written in English. Results Of 1234 potential articles, 52 papers were included. Only studies using TMS were found. BM included immune and endocrine serum markers, neuroimaging techniques and electrophysiological outcomes. In 12 articles (21.4%) endpoint BM measurements were not significantly associated with clinical outcomes. All studies reached significant results in the main clinical rating scales. BM outcomes were used as predictors of response, to understand mechanisms of TMS, and as a surrogate of safety. Conclusions fMRI, SPECT, PET, MRS, cortical excitability and BDNF consistently showed positive results. BDNF was the best predictor of patients’ likeliness to respond. These initial results are promising; however, all studies investigating BM are small, used heterogeneous samples, and did not take into account confounders such as age, gender or family history. Based on our findings we recommend further studies to validate BM in non-invasive brain stimulation trials in MDD.