Bipolar and unipolar depression are two common mental conditions. The depressive manifestation in both disorders is identical. However, bipolar and unipolar depression require different psychopharmacological treatment. Currently, all patients with depression who have not undergone a manic condition will be diagnosed as suffering from unipolar depression and treated accordingly. This will pose a risk of inducing a manic episode in bipolar depressed subjects. Therefore, establishing a diagnosis of bipolar depression prior to the expression of a manic episode would be highly beneficial. Technological advances in functional neuroimaging have enabled shedding light on the mechanisms underlying affective disorders. In this review, we present a comparison of functional neuroimaging findings between patients who suffer from unipolar and bipolar depression during both symptomatic and euthymic phases of their disease. Most studies focused on two core domains of depression - emotion processing and executive control, and on associated anatomical structures in the limbic system and the prefrontal cortex, respectively. The long-term goal of research on this topic has been to find objective state and trait neuroimaging markers that can be used to improve diagnostic reliability regarding these two subtypes of depression that currently cannot be teased apart clinically.