In this work, 25 Parkinson’s disease patients and 24 healthy controls (HC) were scanned in order to quantify brain iron content in eight major deep gray matter structures. In addition to comparing global iron deposition, a novel threshold-based method was used to assess regional high iron (RII) in these nuclei. Among all the structures, the substantia nigra (SN) was the only one showing significantly higher iron content in PD patients compared to that of the HC cohort with the regional analysis revealing more prominent results. There are two populations of PD patients, those that do not change iron content in SN and those that do. For the abnormally high SN iron content group, there was a significantly higher UPDRS-III than the group showing normal iron content.