The striatum is a heterogeneous brain structure with microstructural gradients along its main axes. Changes in its organization are associated with Parkinson’s disease (PD). Yet the spatial variability in the human striatum is not well characterized and is mostly limited to animal and postmortem studies. We developed a non-invasive MRI method for measurement of microstructural gradients along axes of the striatum in individuals in vivo. Using clinical data, we found a T1w/T2 gradient along the anterior-posterior axis of the putamen, which is decreased in PD. This decrease explains the patients’ asymmetries in dopamine loss and motor symptoms.