Aim: To investigate the association between cognitive impairment and gray/white matter volume abnormalities in pediatric patients with Turner syndrome (TS) presenting with various karyotypes. Methods: In the present study, 21 pediatric patients with TS and the 45, X karyotype, 24 pediatric patients with TS and other karyotypes, and 20 normal healthy controls, underwent the Wechsler intelligence test, behavioral testing, and a 3.0T magnetic resonance (MR) scan. Whole-brain high-resolution T1-weighted images were processed with SPM8 software and analyzed using voxel-based morphometry (VBM); differences in gray/white matter volume between the TS groups and healthy controls were compared using analysis of covariance. Results: Pediatric patients in both TS groups had significantly lower IQ scores compared to the normal controls (p<0.05). Furthermore, both TS groups scored significantly less than the normal controls in various composite tests of cognitive function, including verbal comprehension, perceptual reasoning, working memory, and processing speed (p<0.05). There were no significant differences between the two TS patient groups in terms of their scores for verbal comprehension, perceptual reasoning, working memory, and processing speed. However, they did display significant differences in the following tests: accuracy and reaction times in the executive control test, reaction times in the short-, middle-, and long-term attention test, and accuracy in the long-term attention test. Patients in the 45, X karyotype group displayed decreased gray matter volume in the bilateral cuneus, calcarine sulcus postcentral gyrus, right precuneus, superior parietal lobule, lingual gyrus, left precentral gyrus, and cingulate gyrus. However, gray matter volume was increased in the bilateral dorsal midbrain, orbital frontal gyrus, left insular lobe, superior temporal gyrus, inferior temporal gyrus, parahippocampal gyrus, cerebellum, posterior insular lobe, right caudate nucleus, putamen, and temporal pole. Patients with TS with other karyotypes exhibited decreased gray matter volume in the left precuneus, cingulate gyrus, right postcentral gyrus, supramarginal gyrus, angular gyrus, and cuneus; contrastingly, gray matter volume increased in both the epencephals, left caudate nucleus, superior temporal gyrus, right insular lobe, and temporal pole. All volume differences were statistically significant when compared with normal controls [familywise error (FWE)-corrected p<0.05]. With regard to the two TS groups, gray matter volume in the left hippocampus and left caudate nucleus was significantly decreased in the 45, X karyotype group compared to patients with TS with other karyotypes (FWE-corrected p<0.05); conversely, gray matter volume in the right supramarginal gyrus was increased in the 45, X karyotype group (FWE-corrected p<0.05). Conclusion: Pediatric patients with TS display a lower level of intelligence compared to healthy controls, this is complicated by verbal and non-verbal cognitive impairment. The neuropathological basis of such cognitive deficiencies may be as a result of abnormalities in gray matter development.