Adverse maternal events around the time of conception influence embryonic development. Thus, aberrations in the uterine environment during early pregnancy, such as those resulting from maternal metabolic or nutritional disruption, can alter gene expression in the developing embryo, leading to variations in its developmental trajectory. Dietary supplementation of long-chain omega-3 polyunsaturated fatty acids (LCPUFA), especially Docosahexaenoic acid (DHA) improves metabolic and reproductive health across species. The objective of this study was to evaluate the effects of peri-conceptual LCPUFA supplementation on endometrial gene expression, uterine health and embryonic gene expression in overweight horses. Thirteen non-lactating light horse mares (mean ± SEM age=13.56±0.11 yr; mean ± SEM BCS=7.07±0.21) were supplemented with concentrate (n=6) or an isocaloric diet containing 0.06 g/kg BW algae-derived omega-3 LCPUFA (n=7) beginning 60 d prior to sample collection. Four consecutive ovulatory cycles were monitored, and uterine endometrial samples were obtained 12 d post-ovulation in cycles 1, 3 and 4. Mares were bred and embryos were flushed 12 d post ovulation 2,3 and 4. Endometrial biopsies obtained from supplemented mares contained increased DHA and omega-3 fatty acids as a percent of total fat (P< 0.05). Endometrial biopsy scores were assigned to endometrial tissues and mares receiving the LCPUFA supplementation had improved scores during the first ovulatory period as compared to control animals (P=0.009). Candidate genes essential to inflammation, prostaglandin synthesis and embryonic development were evaluated by quantitative reverse transcriptase polymerase chain reaction. Data were log transformed and analyzed using the GLM procedure in SAS (v9.3). When examining the data independent of breeding and pregnancy status, endometrial obtained samples from LCPUFA supplemented mares contained reduced IL6 (P= 0.04) and TNFa (P=0.03) mRNA abundance and tended to have increased transcript abundance for Uterocalin (P= 0.09), SAA (P= 0.06) and IL10 (P= 0.06). Endometrial samples from mares fed LCPUFA pregnant in cycle 3 contained greater IL10 (P< 0.001), PTGFS (P=0.05), OXTR (P=0.05) and PLA2G3 mRNA (P= 0.009) and had a tendency for increased SAA (P= 0.08), PTGES (P=0.10) and SLCO2A1 (P=0.10) mRNA abundance. Supplemented mares bred but not pregnant at day 12 in cycle 3 had reduced expression of PTGER2 (P=0.001) and PTGS1 (P= <0.001) in endometrial samples. In embryos obtained post ovulatory cycle 3 and 4, relative transcript abundance of GATA4 and GATA6, markers of endoderm differentiation, along with GATA3 and ELF3, markers of trophectoderm differentiation were greater (P< 0.05) in embryos from LCPUFA supplemented mares (n=5), than controls (n=5). These results indicate that algae-derived LCPUFA supplementation during the peri-conceptual period alters the post-ovulatory uterine environment in the horse by modifying expression of genes related to inflammation and regulating prostaglandin synthesis. Additionally, embryos obtained from supplemented mares displayed differential gene expression related to embryonic lineage specification.