We examined the contribution of candidate genes for Alzheimer’s disease (AD) on Chromosome 21 and other chromosomes to differences in Aβ peptide levels in a cohort of adults with DS, a population at high risk for AD. Participants were 254 non-demented adults with Down syndrome, 30–78 years of age. Genomic DNA was genotyped using an Illumina GoldenGate custom array. We used linear regression to examine differences in levels of Aβ peptides associated with the number of risk alleles, adjusting for age, sex, level of intellectual disability, race/ethnicity and the presence of the APOE ε4 allele. For Aβ42 levels, the strongest gene-wise association was found for a SNP on CAHLM1; for Aβ40 levels the strongest gene-wise associations were found for SNPs in IDE and SOD1, while the strongest gene-wise associations with levels of the Aβ42/Aβ40 ratio were found for SNPs in SORCS1. Broadly classified, variants in these genes may influence APP processing (CALHM1, IDE), vesicular trafficking (SORCS1), and response to oxidative stress (SOD1).