Apolipoprotein E (APOE) isoforms differentially regulate brain amyloid-β (Aβ) peptide clearance. The APOE ε4 allele is the strongest genetic risk factor for late-onset Alzheimer’s disease (AD), increasing risk and reducing age of onset, while the APOE ε2 allele confers protection. In a cohort of cognitively normal individuals, biomarkers of cerebral Aβ deposition varied according to APOE genotype. In a mouse model of β-amyloidosis expressing human APOE isoforms, Aβ concentration and clearance in brain interstitial fluid (ISF) depended on the isoform. APOE isoform-dependent differences in soluble Aβ metabolism were observed in both aged and young mice. Amyloidogenic processing of amyloid precursor protein (APP) and Aβ synthesis did not vary according to APOE isoform in young mice. Results suggest that APOE alleles contribute to AD risk by differentially regulating Aβ clearance, indicating that Aβ clearance pathways may be useful therapeutic targets for AD prevention. The study provides in vivo evidence that APOE isoform-dependent differences in Aβ clearance modulate the onset of Aβ accumulation in transgenic mice and humans. APOE isoform-dependent differences in Aβ concentration and clearance were observed before Aβ deposition. Amyloidogenic processing of APP did not vary according to APOE isoform. Rates of Aβ synthesis did not differ according to APOE isoform. The study highlights the role of APOE in regulating Aβ clearance and suggests that APOE genotype may influence Aβ accumulation through differential regulation of Aβ clearance.Apolipoprotein E (APOE) isoforms differentially regulate brain amyloid-β (Aβ) peptide clearance. The APOE ε4 allele is the strongest genetic risk factor for late-onset Alzheimer’s disease (AD), increasing risk and reducing age of onset, while the APOE ε2 allele confers protection. In a cohort of cognitively normal individuals, biomarkers of cerebral Aβ deposition varied according to APOE genotype. In a mouse model of β-amyloidosis expressing human APOE isoforms, Aβ concentration and clearance in brain interstitial fluid (ISF) depended on the isoform. APOE isoform-dependent differences in soluble Aβ metabolism were observed in both aged and young mice. Amyloidogenic processing of amyloid precursor protein (APP) and Aβ synthesis did not vary according to APOE isoform in young mice. Results suggest that APOE alleles contribute to AD risk by differentially regulating Aβ clearance, indicating that Aβ clearance pathways may be useful therapeutic targets for AD prevention. The study provides in vivo evidence that APOE isoform-dependent differences in Aβ clearance modulate the onset of Aβ accumulation in transgenic mice and humans. APOE isoform-dependent differences in Aβ concentration and clearance were observed before Aβ deposition. Amyloidogenic processing of APP did not vary according to APOE isoform. Rates of Aβ synthesis did not differ according to APOE isoform. The study highlights the role of APOE in regulating Aβ clearance and suggests that APOE genotype may influence Aβ accumulation through differential regulation of Aβ clearance.