IMPORTANCE: Several studies suggest that the apolipoprotein E (APOE) epsilon4 allele modulates cerebrospinal fluid (CSF) levels of beta-amyloid 42 (Abeta42). Whether this effect is secondary to the association of the APOE epsilon4 allele with cortical Abeta deposition or whether APOE epsilon4 directly influences CSF levels of Abeta42 independently of Abeta pathology remains unknown. OBJECTIVE: To evaluate whether the APOE genotype affects the diagnostic accuracy of CSF biomarkers for Alzheimer disease (AD), in particular Abeta42 levels, and whether the association of APOE epsilon4 with CSF biomarkers depends on cortical Abeta status. DESIGN, SETTING, AND PARTICIPANTS: We collected data from 4 different centers in Sweden, Finland, and Germany. Cohort A consisted of 1345 individuals aged 23 to 99 years with baseline CSF samples, including 309 with AD, 287 with prodromal AD, 399 with stable mild cognitive impairment, 99 with dementias other than AD, and 251 controls. Cohort B included 105 nondemented younger individuals (aged 20-34 years) with CSF samples available. Cohort C included 118 patients aged 60 to 80 years with mild cognitive symptoms who underwent flutemetamol F 18 ([18F]flumetamol) positron emission tomography amyloid imaging and CSF tap. EXPOSURES: Standard care. MAIN OUTCOMES AND MEASURES: Cerebrospinal fluid levels of Abeta42 and total and phosphorylated tau in relation to the APOE epsilon2/epsilon3/epsilon4 polymorphism in different diagnostic groups and in cases with or without cortical uptake of [18F]flutemetamol. RESULTS: The CSF levels of Abeta42 but not total and phosphorylated tau were lower in APOE epsilon4 carriers compared with noncarriers irrespective of diagnostic group (cohort A). Despite this, CSF levels of Abeta42 differed between participants with AD when compared with controls and those with stable mild cognitive impairment, even when stratifying for APOE genotype (P < .001 to P = .006). Multiple binary logistic regression revealed that CSF levels of Abeta42 and APOE epsilon4 genotype were independent predictors of AD diagnosis. In cohort B, APOE epsilon4 carrier status did not influence CSF levels of Abeta42. Moreover, when stratifying for cortical uptake of [18F]flutemetamol in cohort C, APOE epsilon4 genotype did not influence CSF levels of Abeta42. This result was replicated in a cohort with individuals from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) using carbon 11-labeled Pittsburgh Compound B scanning. CONCLUSIONS AND RELEVANCE: Cerebrospinal fluid levels of Abeta42 are strongly associated with the diagnosis of AD and cortical Abeta accumulation independent of APOE genotype. The clinical cutoff for CSF levels of Abeta42 should be the same for all APOE genotypes.