Parkinson's disease (PD) is characterised by dopaminergic neuronal loss and iron overload in the nigrostriatum. Diffusion Kurtosis Imaging (DKI) and Quantitative Susceptibility Mapping (QSM) allow quantification of alterations in tissue microstructure based on water diffusion and iron deposition respectively. Our case-control study in PD using DKI revealed greater cellular loss in the lateral SN and complex microstructural degradation in the putamen. QSM showed spatially variant iron deposition (Δχ) in the grey nuclei congruent with histochemical reports, and multivariate analysis showed that putaminal and lateral nigral Δχ significantly predicted UPDRS. Significant correlations between Δχ and DKI indices were found in the putamen.