Introduction Anti-inflammatory properties of fish-oil are well known and suggested during pregnancy. MMP-1 is involved in inflammation and tissue remodelling. There have been studies focused on anti-inflammatory effect of maternal omega use on human milk while little is known about the effect of omega use on breastmilk proteases. Leptin is an important hormone that influences MMP levels in various tissues and exerts its metabolic effects. In our study we assessed the levels of MMP-1, TIMP-1, leptin, IL-6 and FA's including PUFA in breastmilk from women who used omega-3. Materials and methods Our study was a cross-sectional study included 67(Group 1,n = 32, omega user; Group 2n = 35, non-user)lactating women and their infan MMP-1, TIMP-1, leptin, IL-6 and FA's were evaluated in breastmilk of both groups. MMP-1, TIMP-1, IL-6 and leptin were measured by enzyme-linked immunoabsorbent assay (ELISA) method. Breastmilk fatty acids were measured by gas chromatography flame ionisation detector (GC-FID). Results Matrix metalloproteinase-1 (MMP-1) levels in breastmilk were significantly lower in breastmilk from omega users (mean +/- SD, 0.455 +/- 0.1) than non-users (mean +/- SD, 0.677 +/- 0.289) (p=.0001). MMP-1 and omega 6:3 ratio were positively correlated (r: 0.301,p=.01). MMP levels were correlated with IL-6 (Pearson'sr: 0.411,p<.001). MMP-1 and leptin levels were positively correlated (r: .388,p=.001). Conclusion MMP-1 levels in breastmilk, may be modified by maternal omega use in pregnancy which may help to redirect extracellular matrix remodelling and metabolic programming in early infancy.