Major depression is one of the most frequent and serious psychiatric diseases. Although the disease is highly heritable, the search for candidate genes has been of limited success hitherto. The complex, polygenetic hereditary transmissions coding for heterogeneous, clinically defined phenotypes such as major depression may be better identified using the endophenotype approach. A recent study, reporting an association of the risk allele in a serotonin transporter polymorphism (5-HTTLPR) with increased amygdala responsiveness to aversive stimuli, stimulated the new research field of imaging genetics, which is characterized by the choice of neurobiological activity patterns as endophenotypes. This review discusses recent studies from this rapidly growing research field, focussing on genetic effects on cortico-limbic circuitries during emotion processing. Evidence is reviewed suggesting that potential risk-alleles for depression are associated with functional cortico-limbic abnormalities, which frequently occur in patients with major depression.