Late-onset Alzheimer´s Disease (AD) is the most common type of dementia and it appears to be caused by defective clearance of amyloid β in the brain. It is known that polymorphisms in the APOEgene are the major genetic risk factor. Carriers of two APOE4alleles (APOE4/4) have 15 times higher risk to develop AD than homozygous carriers of the most common allele APOE3 (APOE3/3). Here, we generated isogenic induced pluripotent stem cell (iPSC) lines with different APOEgenotypes (APOE4/4and APOE3/3) using CRISPR/Cas9 editing. Following characterisation (pluripotency, genotyping and karyotyping), cells were differentiated into cerebral organoids for assessment of amyloid secretion and phosphorylation of Tau. After 6 months in culture,the pathological forms of amyloid β 1-42 and 1-40 were detected in organoid lysates and in secreted media with no statistical difference between organoids of different APOE genotypes. However, levels of amyloid β 1-42 were slightly higher in APOE4/4 than APOE3/3 in lysates (2.71±0.68 vs 1.70±0.78 pmol/L, n=5-7) and secreted media (0.86±0.19 vs 0.39±0.11 pmol/L, n=7). Total Tau protein was also detected in organoid lysates and secreted media with no statistical difference between group. Levels of phosphorylated Tau at different amino acid sites were detected in organoid lysates but not in secreted media. Our data thus provides a quantitative snapshot of levels of amyloid and Tau in isogenic APOE cerebral organoids.