The objective of this paper is to assess abnormal phase values, indicative of increased iron content, using susceptibility-weighted imaging (SWI)-filtered phase of the subcortical deep gray matter (SDGM) in adolescent multiple sclerosis (MS) and other neurological disorders (OND) patients, and in healthy controls (HC). Twenty adolescent MS and eight adolescent OND patients and 21 age- and sex-matched HC were scanned on a 3T GE scanner. Mean phase of abnormal phase tissue (MP-APT), MP-APT volume, normal phase tissue volume (NPTV) and normalized volume measurements were obtained for total SDGM, as well as specific structures separately. Significantly increased MP-APT (28.2%, p<.001) and MP-APT volume (82.7%, p<.001), and decreased NPTV (-23.3%, p<.001) and normalized volume (-15.5%, p<.001) in the pulvinar nucleus of the thalamus was found in MS patients compared to HC. MP-APT in MS patients was also increased in total SDGM (p=.012) and thalamus (p=.044). Compared to OND patients, MS patients had increased MP-APT volume in the pulvinar nucleus of the thalamus (p=.044) and caudate (p=.045). Increased MP-APT of the SDGM structures were associated with increased T2 and T1 lesion burden and brain atrophy in MS patients. Adolescent MS patients showed increased iron content in the SDGM compared to OND patients and HC.