© 2019 Elsevier Ltd The effect of fermentation on the antithrombotic properties of polar lipids in ovine milk has been assessed through the production of yoghurts. The total lipids (TL), total neutral lipids (TNL), and total polar lipids (TPL) were extracted. The fatty acid profiles of all yoghurt polar lipids were analysed by GC-MS. The levels of MUFA increased in the fatty acids of the polar lipids, but there was a reduction in PUFA as milk was fermented to yoghurt. The bioactivity of each lipid extract was assessed against platelet-activating factor (PAF) induced platelet aggregation. All yoghurt polar lipids exhibited potent antithrombotic activities with IC 50 values ranging from 45 to 77 µg. Shotgun metagenomics determined the species-level microbial composition and functional potential of the yoghurts. Yoghurts containing L. acidophilus seem to correlate with greater bioactivity. Several phospholipid biosynthetic genes have been identified in the most antithrombotic yoghurts. This study has demonstrated that fermentation enhances the antithrombotic properties of yoghurt polar lipids against PAF.