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The theme of the Self helps to enlighten the relationship «by difference» between psychoanalysis and neuroscience. They in fact investigate human subjectivity by different methods, conceptual and linguistic systems. The different psychoanalytical models of the Self easily converge towards an unified theory of subjectivity. The aim of founding this theory to a neurobiological ground encounters great empirical and logical difficulties. The «correlationism» driving the comparisons between psychoanalysis and neuroscience subtends the neurobiological foundation of psychoanalysis and its ontological and methodological subordination to neuroscience. The relationship between the two disciplinary areas proposed in this work is based instead on the principle of the difference of perspectives and of the complexity of reality. It substitutes the aim of the reduction-identification of psychoanalytical with neurobiological concepts with an epistemological pluralism promoting their dialectical confrontation in sight of the continuos deepening of the knowledge of human subjectivity.