Cows were fed a control diet with no added lipid, or diets containing SO or FO (n = 5 cows/group). The objective was achieved by supplementing dairy cows with soybean oil (SO high in linoleic acid) or fish oil (FO high in EPA and DHA) for 63 days (nine weeks). The objective of this study was to determine the effect of long-term supplementation of unsaturated oil on lipid metabolism and transcription of genes involved in lipid metabolism in subcutaneous adipose tissue (SAT) of mid-lactating dairy cows. Our results suggest that it is the effects of lipid metabolism rather than the urea concentration which probably alter the rate of involution and innate immune response, in turn influencing subsequent fertility. Examination of the genes/pathways involved suggests that plasma urea levels may reflect variations in lipid metabolism. LPS increased S100A8 expression as expected but urea treatment had no effect on expression of any tested gene. These were treated with 0, 2.5, 5.0 or 7.5 mmol/L urea, equivalent to low, medium and high circulating values with or without challenge by bacterial lipopolysaccharide (LPS). Study 2 investigated the relationship between urea concentration and expression of 6 candidate genes (S100A8, HSP5A, IGF1R, IL17RB, BRINP1, CRISPLD2) in bovine endometrial cell culture. These were predominantly associated with tissue turnover (e.g., BRINP1, FOXG1), immune function (e.g., IL17RB, CRISPLD2), inflammation (e.g., C3, SERPINF1, SERPINF2) and lipid metabolism (e.g., SCAP, ACBD5, SLC10A). The biological functions of 781 mapped genes were analysed using Ingenuity Pathway Analysis. Study 1 used microarray analysis to identify genes whose endometrial expression 2 weeks postpartum correlated significantly with the mean plasma urea per cow, ranging from 3.2 to 6.6 mmol/L. The rate of involution and the endometrial ability to mount an adequate innate immune response after calving are both critical for subsequent fertility. Both high and low circulating urea concentrations, a product of protein metabolism, are associated with decreased fertility in dairy cows through poorly defined mechanisms.