The relations between psychoanalysis and neuroscience have undergone considerable changes during the last two decades. From the cool distance that was maintained on both sides, a new neuroscientific basis has emerged for a dialogue between psychoanalysis and neuroscience. A crucial question then arises about the identity of psychoanalysis in this dialogue. What will be the effects of the growing impact of neuroscientific discoveries on psychoanalysis? Freud regarded psychoanalysis and the natural sciences as having a similar epistemological foundation determined by their relation to unknown aspects of reality. The author proposes that this viewpoint creates equal ground for psychoanalysis and neuroscience in their evolving mutual relationships. In the clinical realm, however, psychoanalysis cannot work without clinical, developmental, and metapsychological premises, which render clinical ontological autonomy to psychoanalysis in its relationship with the other sciences. This fact also needs to be taken into account when brain imaging techniques are applied to outcome research of psychotherapy.