The apolipoprotein E gene (APOE) is expressed as three major isoforms, APOE ε2, ε3 and ε4 that encode the apoE2, E3 and E4 proteins, respectively. APOE ε4 is associated with an increased risk for age-related neurodegenerative diseases including Alzheimer’s disease (AD) and dementia with Lewy bodies (DLB), and increases the risk of dementia in Parkinson’s disease (PD), however, the exact molecular mechanisms underpinning the associations between APOE ε4 and neurodegeneration are still unknown. Pathologically, α-synuclein (αSyn) is the primary component of Lewy neuropathology which is stereotypically found in PD, DLB and also in the majority of AD brains upon post mortem examination, and changes in the soluble levels of intra- and extracellular αSyn in the central nervous system have been found in AD patients compared to cognitively healthy individuals. With this in mind, we hypothesized that interactions, both direct and indirect, between apoE4 / APOE ε4 and αSyn might help explain their associations with the pathogenesis of multiple neurodegenerative diseases. Using mouse models with a humanized APOE ε4/ε4 or ε3/ε3 liver genotype we found that changing the liver genotype to APOE ε4/ε4 led to a re-compartmentalization of brain αSyn and significant changes in key pre- and postsynaptic protein levels We also found that in prodromal sporadic AD patients APOE ε4 carriers had significantly increased cerebrospinal fluid (CSF) αSyn levels, and in autosomal dominant AD APOE ε4 carriers higher CSF αSyn levels that were correlated with AD-onset and increasing brain amyloid-β plaque deposition. When next assessing any disease related changes in the molecular sizes of αSyn and apoE in AD and PD post mortem brain parenchyma we found that the amygdala had a differing distribution of αSyn and apoE4 species. Co-incubation of the recombinant apoE isoforms and αSyn led to high molecular weight αSyn species, increased high molecular weight apoE2 species and a stabilized pool of monomeric apoE3. Using, binding kinetics assays and human neuronal cell cultures we found that recombinant apoE isoforms bind with similar strength to αSyn and reduce αSyn cellular uptake, whereas astrocyte secreted apoE led to an apoE- isoform-dependent reduction in αSyn uptake (apoE4 > apoE3 > apoE2). Further, heparin sulfate proteoglycans were partially responsible for αSyn uptake mediated by apoE. Taken together, our results show that APOE / apoE is linked to changes in levels, species and compartmentalization of αSyn in multiple pathological contexts ranging from the central nervus system to the periphery in humans, mouse models and cell lines. Our data reinforce the growing body of literature linking APOE / apoE and αSyn to the pathogenesis of the most prevalent neurodegenerative diseases.