The objectives of the present study were to evaluate the effect of conjugated linoleic acid (CLA t10, c12, C18:2), linolenic acid (C18:3) and docosahexaenoic acid (DHA, C22:6) supplementation on in vitro bovine embryo development, embryo survival after cryopreservation, gene expression and AMPKα phosphorylation. Control groups with modified synthetic oviduct fluid (mSOF) ± 100 μM β-mercaptoethanol (β-ME) were performed. The effects of co-culture with bovine oviduct epithelial cell (Boec) monolayers, serum supplementation and embryo development in the ewe oviduct, on gene expression were also examined. Experiments 1 and 2: a lower d 7 embryo survival was found with 100 μM C22:6 and 100 μM C18:2 supplementation compared to 1 μM C22:6 and 100 μM β-ME supplementation ( P < 0.05). C18:3 supplementation had no effect on d 7 embryo survival, but 100 μM C18:3 increased d 8 embryo survival compared to 100 μM β-ME supplementation ( P < 0.05). Experiments 3 and 4: stearoyl-CoA desaturase 1 (SCD1) and sterol regulatory element-binding transcription factor 1 (SREBP1) mRNA decreased after 10 μM C22:6 supplementation compared to all other supplementations ( P < 0.05). A lower fatty acid desaturase 2 (FADS2) transcript level was found with 100 μM C18:2, 10 μM C22:6 and 10 μM C18:3 supplementations compared to groups without fatty acid supplementation ( P < 0.05). Acetyl-CoA-carboxylase (ACC), fatty acid synthase (FAS), adipose differentiation-related protein (ADRP), acyl-CoA synthetase long-chain family member 1 (ACSL1), diacylglycerol O-acyltransferase 1 (DGAT1), carnitin palmitoyltransferase-II (CPT-II) mRNAs expression and AMPKα phosphorylation were not modified with PUFA supplementation. Experiment 5: SCD1 and FAS mRNA decrease in Boec group compared to serum supplementation, as SCD1 mRNA in ewe oviduct group ( P < 0.05). In conclusion, this study showed that a PUFA supplementation with C18:2, C18:3 or C22:6 in bovine culture development for 6 days and co-culture with Boec down-regulate mRNA expression of proteins involved in lipid metabolism in d 7–8 embryo (SCD1 and FADS2 desaturases), probably through SREBP1 mRNA regulation after 10 μM C22:6 supplementation, indicating a modification of saturated/unsaturated fatty acid balance in bovine blastocyst.