The follicular fluid (FF) microenvironment consists of serum components and follicular cell secretions, which are essential for oocyte maturation, preparing it for fertilization. Although very important, the biochemical composition of the follicular fluid is still poorly characterised. The hypothesis is that the lipid composition of the follicular fluid on Day 6 post-artificial insemination (AI) is different between cows diagnosed as pregnant (P) or not pregnant (NP) on Day 30 post-AI. The objectives were to (1) evaluate the influence of follicle aspiration procedure performed on Day 6 post-AI on pregnancy rates and (2) characterize the lipid profile of the FF collected on Day 6 in pregnant (P) and nonpregnant (NP) cows, in order to associate the amount of molecules in the FF with the probability of conception. Eighty-two multiparous Nelore cows, between 40 and 45 days post-partum and body condition score between 4 and 6 (1 to 9 scale) were used. Fixed-time AI was performed in all the animals and 6 days post-AI the animals were divided in control group, in which animals were not manipulated (CG, n = 41), and aspiration group (AG, n = 41) from which follicular fluid was aspirated from the largest follicle present in either one of the ovaries. The FF was centrifuged and stored at –80°C. Pregnancy diagnosis was performed by ultrasonography 30 days post-AI. Results showed pregnancy rates of 53% for the AG and 56% for the CG, suggesting no detrimental effect of the follicle aspiration procedure on the success of pregnancy (Kruskal-Wallis test). A pool of the FF samples from the P and NP cows was analyzed by mass spectrometry (MS), using the high-resolution shotgun lipidomics (HRSL) approach in order to compare the lipid profile between groups. Despite the fact that HRSL is not quantitative but qualitative, the general levels of the different lipid classes can be compared between groups of study and the differences in the abundance of the ions of each lipid class can be expressed as percentage. Taking this into account, in negative mode MS, the NP group showed an increase of 300% in the levels of free fatty acids such as palmitic, oleic, and linoleic acids compared to the P group as well as an increase of 50% in the levels of phospholipids and two new species of phospholipids (phosphatidylcholine and phosphatidylserine) could be observed. Furthermore, animals from the P group showed an increase of 130% in the content of structural fatty acids such as ceramids and triacylglycerols. Our findings suggest that there is a difference between the amount of lipid classes and in the lipid species origins present in the follicular fluid of cows that were P or NP on Day 30 post-AI.