Choline is a vital nutrient that is used by the body to produce acetylcholine, which is an important neurotransmitter essential for brain and nervous system functions. Therefore, sufficient intake of dietary choline is important for proper brain function and neurodevelopment. It is especially critical for brain development during the perinatal period. This study investigated the impact of perinatal maternal choline supplementation (MCS) in Ts65Dn mice, which is a mouse model of Down syndrome and Alzheimer’s disease. The breeder pairs were assigned to receive 1 of 2 choline-controlled experimental diets. The control rodent diet contained 1.1 g/kg choline chloride, while the choline-supplemented diet contained 5.0 g/kg choline chloride. The dataset contains gene expression level changes due to MCS in 6 and 11 month old mice, MCS-driven gene expression level changes overlapped during aging in 2N and Ts65Dn mice, gene expression level changes regardless of genotype or age, and NanoString nCounter analysis.