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We treated a thirteen year old boy for life-threatening self-injurious behavior (SIB) and severe Kanner’s autism with Deep Brain Stimulation (DBS) in the amygdaloid complex as well as in the supra-amygdaloid projection system. Two DBS-electrodes were placed in both structures of each hemisphere. The stimulation contacts targeted the paralaminar, the basolateral, the central amygdala as well as the supra-amygdaloid projection system. DBS was applied to each of these structures, but only stimulation of the baso-lateral part proved effective in improving SIB and core symptoms of the autism spectrum in the emotional, social and even cognitive domains over a follow up of now 24 months. These results, which have been gained for the first time in a patient, support hypotheses, according to which the amygdala may be pivotal in the pathogeneses of autism and point to the special relevance of the baso-lateral part.