ObjectivePositive α-synuclein seed amplification assay (SAA) is a biomarker found in most people with Parkinson's disease (PD). We explored if free-water (FW) imaging detects microstructural differences in the brains of patients with early PD with SAA+ or SAA- status.MethodsWe studied patients with PD with baseline diffusion imaging and α-synuclein SAA data from the Parkinson's Progression Markers Initiative (PPMI). We compared FW, FW corrected fractional anisotropy (FAT), and clinical characteristics between SAA+ and SAA- groups. We also applied the Automated Imaging Differentiation for Parkinsonism (AIDP) at baseline to classify PD versus atypical parkinsonism, stratified by SAA status.ResultsAmong 462 participants (41 SAA- and 421 SAA+), individuals with SAA+ had hyposmia and shorter motor symptom duration before baseline magnetic resonance imaging (MRI). AIDP identified PD in 92.4% (n = 427, 91.6% had SAA+) and classified 7.6% as atypical parkinsonism (n = 35, 85.7% had SAA+). At baseline, SAA+ individuals had lower FW in the superior cerebellar peduncle, compared to SAA- (pFDR < 0.05). No significant differences in FAT were found between groups.InterpretationPositive α-synuclein SAA was associated with focal microstructural differences but did not distinguish broader diffusion MRI (dMRI) changes across FW and FAT metrics. These findings indicate that molecular confirmation of synuclein aggregation (via SAA) provides limited stratification of neurodegeneration detected by FW imaging in early PD. ANN NEUROL 2026.