The purpose of this review was to investigate the neurophysiological and neuroimaging characteristics of patients with depression and anxiety reported in previous studies. A literature search was conducted using Medline and psychiatric textbooks. "Electroencephalography (EEG)", "Event Related Potentials (ERP)", "functional neuroimaging", "heart rate variability (HRV)" and "depression or anxiety" were used as key words. A physiological finding indicated that there was a higher degree of relativity with regards to prefrontal dysfunction in patients with depression. Right prefrontal lobe hyperactivity and left prefrontal hypoactivity were consistently observed, and abnormalities were observed in other regions (ACC, hippocampus, amygdala, etc.). Therefore, dysfunctions in these areas are related to depressive symptoms. In patients with anxiety disorder, each emotional condition showed specific activation patterns in different brain regions, such as the prefrontal cortex, occipital lobe, temporal lobe, hippocampus, and limbic system, including the amygdala. However, in the majority of patients with anxiety disorder, the degree of activation was higher in the right hemisphere than in the left hemisphere. The current data supports that there is a difference in brain dysfunction characteristics between depression and anxiety and that the different activations of various brain regions would play a significant role in the pathophysiology of depression and anxiety disorder.