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The 16p11.2 distal CNV predisposes carriers to e.g., autism spectrum disorder and schizophrenia. We compared subcortical brain volumes of 12 16p11.2 distal deletion and 12 duplication carriers to 6882 non-carriers from the large-scale brain Magnetic Resonance Imaging collaboration, ENIGMA-CNV. After stringent CNV calling procedures, and standardized FreeSurfer image analysis, we found negative dose-response associations with copy number on intracranial volume and on regional caudate, pallidum and putamen volumes (<jats:italic>\u03b2<\/jats:italic>\u2009=\u2009\u22120.71 to \u22121.37; <jats:italic>P<\/jats:italic>\u2009&lt;\u20090.0005). In an independent sample, consistent results were obtained, with significant effects in the pallidum (<jats:italic>\u03b2<\/jats:italic>\u2009=\u2009\u22120.95, <jats:italic>P<\/jats:italic>\u2009=\u20090.0042). The two data sets combined showed significant negative dose-response for the accumbens, caudate, pallidum, putamen and ICV (<jats:italic>P<\/jats:italic>\u2009=\u20090.0032, 8.9\u2009\u00d7\u200910<jats:sup>\u22126<\/jats:sup>, 1.7\u2009\u00d7\u200910<jats:sup>\u2212<\/jats:sup><jats:sup>9<\/jats:sup>, 3.5\u2009\u00d7\u200910<jats:sup>\u221212<\/jats:sup> and 1.0\u2009\u00d7\u200910<jats:sup>\u22124<\/jats:sup>, respectively). Full scale IQ was lower in both deletion and duplication carriers compared to non-carriers. 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