Feeding flaxseed to dairy cows can modulate gene expression and PG synthesis in the uterus at the time of peri-implantation. The objectives of the present study were to determine which flaxseed components are responsible for these effects and how different endometrial cell types are affected. We evaluated the effects of six different linoleic acid (n-6):α-linolenic acid (n-3) ratios and three concentrations of the lignan enterolactone (ENL) on endometrial stromal cells (SC) and epithelial cells (EC). The mRNA abundance of genes with known or suspected roles in embryo survival or PG synthesis was evaluated, along with PGE2 and PGF2α concentrations in culture media. The mRNA abundance of several genes was modulated by different fatty acid (FA) ratios and/or ENL, and this modulation differed between cell types. The FA4 (FA at an n-6:n-3 ratio of 4) treatment (rich in n-3 FA) increased the mRNA abundance of genes that have positive effects on uterine receptivity and implantation when compared with the FA25 (FA at an n-6:n-3 ratio of 25) treatment (rich in n-6 FA). ENL decreased PGE2 and PGF2α concentrations in both cell types, and this reduction was associated with lower mRNA abundance of the PG synthase genes AKR1B1 and PTGES in SC. The combination of ENL with FA (FA4 treatment) resulted in the greatest reduction in PGF2α concentrations when compared with the addition of FA (FA4) or ENL alone. Because of the known luteolytic properties of PGF2α, a reduction in endometrial PGF2α secretion would favour the establishment and maintenance of pregnancy.