© 2019 Elsevier Ltd The effect of fermentation on the antithrombotic properties of polar lipids in raw and pasteurised caprine milk was assessed through the production of various cheeses using the same starter culture. The total lipids (TL), total neutral lipids (TNL), and total polar lipids (TPL) were extracted from each milk and cheese and the TPL fatty acid profiles were analysed by GC¿MS. It was determined that fermentation influenced the polar lipid fatty acid composition. The milk and cheese polar lipids exhibited potent antithrombotic activities with IC50 values ranging from 79 to 226 µg against platelet-activating factor (PAF) induced platelet aggregation. Finally, shotgun metagenomics determined the species-level microbial composition and functional potential of each milk and cheese. Several microbe-encoded phospholipid biosynthetic genes were identified in the most antithrombotic cheeses. Lactococcus lactis and other microbial species may play a significant role in determining the antithrombotic properties and fatty acid composition of caprine cheese polar lipids.