There is little agreement regarding the approach and optimal p-value threshold of SNPs to calculate genetic risk scores for Alzheimer’s disease (AD). This reflects a fundamental underlying debate on the polygenic versus oligogenic disease architecture. We re-investigated the assumptions underlying the choice of specific p-value thresholds defining genetic loci used to determine polygenic risk scores (PRS). We find the optimal p-value threshold for SNP selection is 0.1, which supports the polygenic architecture of AD. We found that previous studies supporting an oligogenic model of AD did not take account of the reduction of APOE-ε4 allele frequency in older individuals, which skewed the results towards lower p-value thresholds and eclipsed the contribution of genes associated to AD with higher p-values. The polygenic approach to AD is also effective to identify individuals at high or low AD risk, when only APOE-ε3 homozygous individuals are considered. We also introduce the standardisation of PRS against a population data which ensures comparability of the PRS between studies. In conclusion, our work demonstrates that AD is fundamentally a polygenic disease and that stratifying populations for AD risk best takes the full PRS score into account.