Abstract Study question The aim of the study is to identify the autophagic profile and the effects of fatty acid treatments on autophagic activity in preimplantation mouse embryos. Summary answer Autophagic activity varies significantly in early stages of mouse preimplantation development; exposure to fatty acids alters the embryonic autophagy profile. What is known already Obesity is one of the top comorbidities for infertility, and obese individuals have elevated fatty acid levels. In serum, palmitic acid (PA) and oleic acid (OA) are the most abundant saturated and unsaturated fatty acids, respectively. We recently reported that PA impairs blastocyst development, affects mitochondrial reactive oxygen species, triacylglycerol levels, and endoplasmic reticulum stress pathways during mouse preimplantation development. Interestingly, the addition of OA counteracts those effects. Autophagy plays an essential role in embryo development, as knock-out of a key autophagy protein is embryonic lethal. Little is known about the autophagic profile in fatty acid treated mouse preimplantation embryos. Study design, size, duration Pools of 20 – 25 mouse embryos were collected from gonadotrophin super-ovulated and mated CD1 female mice. Two-cell stage embryos were treated with 100 µM PA and 250 µM OA, alone and in combination, and 1.5% bovine serum albumin media (control) within KSOMaa media for 18, 24, and 48 hours in vitro. The detection of various autophagic markers were evaluated by immunofluorescence microscopy and RT-qPCR. Participants/materials, setting, methods mRNA levels of autophagic markers were measured using RT-qPCR with the Taqman primers and Universal PCR Mix. Immunofluorescence staining of LC3 puncta (marker for autophagosome formation) was performed using LC3A/B polyclonal antibody (Invitrogen PA1–16931) and DAPI (4′,6-Diamidino–2-phenylindole dihydrochloride) was used to stain for cell nuclei. Analysis of LC3 puncta was performed using ImageJ software. Images were acquired using an LSM 800 laser scanning confocal microscope. Data analysis was completed by GraphPad Prism software. Main results and the role of chance Mouse preimplantation embryos showed no change in mRNA levels of autophagic markers (Bcln1, ATG3, ATG5, and LC3) relative to the control group after 48-hours exposure of 100 µM PA and 250 µM OA treatments, alone and in combination. The number of LC3 puncta was measured and analyzed as a reflection of autophagic activity in mouse preimplantation embryos. Under the fatty acid-free condition, the average number of LC3 puncta per blastomere was significantly decreased after 18 hours of development (p < 0.005). However, the average number of LC3 puncta per blastomere at 18, 24, and 48 hours were not significantly different from each other (p = 0.2724). Following 100 µM PA and 250 µM OA treatments, alone and in combination, autophagic activity was impacted by the presence of fatty acids. Mouse preimplantation embryos exposed to control and fatty acid treatment groups demonstrated no significant differences in LC3 puncta per blastomere at 18- and 24-hours treatment time (p = 0.5381; p = 0.7829). However, embryos exposed to 48 hours of PA treatment had a significantly greater number of LC3 puncta per blastomere than embryos exposed to 48 hours of OA and PA and OA combination treatments (p < 0.05). Limitations, reasons for caution Although LC3 puncta count (autophagosome formation) is impacted by fatty acid treatment, autophagic flux must be measured to fully investigate autophagic activity during mouse preimplantation development. These processes need to be measured in human embryos cultured in vitro. Wider implications of the findings: Profiling autophagic activity in fatty acid treated mouse preimplantation embryos would guide future investigations on pharmacological modulation of autophagy as a therapeutic intervention for developmentally delayed embryos. With the information gained, we aim to develop strategies to assist overweight and obese patients with their fertility needs. Trial registration number Not applicable