Neuroimaging investigations of the effects of psychotherapies treating posttraumatic stress disorder (PTSD), including eye movement desensitization and reprocessing (EMDR), have reported findings consistent with modifications in cerebral blood flow (CBF; single photon emission computed tomography [SPECT]), in neuronal volume and density (magnetic resonance imaging [MRI]), and more recently in brain electric signal (electroencephalography [EEG]). Additionally in the recent past, EMDR-related neurobiological changes were monitored by EEG during therapy itself and showed a shift of the maximal activation from emotional limbic to cortical cognitive brain regions. This was the first time in which neurobiological changes occurring during any psychotherapy session have been reported, making EMDR the first psychotherapy with a proven neurobiological effect. The purpose of this article was to review the results of functional and structural changes taking place at PTSD treatment and presented during the period of 1999–2012 by various research groups. The reported pathophysiological changes are presented by neuropsychological technique and implemented methodology and critically analyzed.