To review neuroimaging intermediate phenotypes of MDD and their relation to genetic risk variants. A systematic literature search of peer-reviewed English language articels using PubMed ( www.pubmed.org ) was performed. Comprehensive evidence on the influence of serotonergic genes (SLC6A4, HTR1A, MAOA, TPH2) and BDNF on the following neural intermediate phenotypes is displayed: amygdala reactivity, coupling of amygdala-anterior cingulate cortex (ACC) activity, ACC volume, hippocampal volume and serotonin receptor 1A (5-HT1A) binding potential (BP). Intermediate phenotypes may bridge the gap between genotype and phenotype by reducing the impreciseness of psychiatric phenotypes and yield more insights into the underlying biology.