During the past decades, the prevalence of affective disorders has been on the rise globally, with only one out of three patients achieving remission in acute treatment with antidepressants. The identification of physiological markers that predict treatment course proves useful in increasing therapeutic success. On the basis of well-documented, recent findings in depression research, we highlight and discuss the most promising biomarkers for antidepressant therapy response. These include genetic variants and gene expression profiles, proteomic and metabolomic markers, neuroendocrine function tests, electrophysiology and imaging techniques. Ultimately, this review proposes an integrative use of biomarkers for antidepressant treatment outcome.