Fatty acids profile on sheep’s milk was determined in 4 Greek breeds (Karagouniko, Chios, Orini Epirus and Improved Epirus) reared under the same diet and management conditions. Milk samples (n=126) were collected from January to May and fat was extracted from raw milk or butter milk. GC-FID analysis of the lipid revealed the presence of 42 fatty acids (FA). Several lipid quality indices were compared among breeds and levels of lactation stage. Some fatty acids affected significantly by the breed (C16:0, C16-1ω9, C18-3ω-6) and the lactation stage (C14:0, C16-1ω9, C18-2t9t12, C18-4ω-3). Chios breed had higher thrombogenic and hypercholesterolaemic indices than the other breeds. Peroxidisability and atherogenic indices did not differentiate among breeds and lactation stage. A significant increase of ω-3 fatty acids was found in the middle of lactation stage compared with the content of ω-3 at the end of lactation stage. Principal component analysis applied to 42 variables (fatty acids) revealed that 11 significant factors accounted for 79 % of the variability. Discriminant analysis considering the breed as classification factor, developed two significant discriminating functions with a 80.16% of correct classification. Considering lactation stage as the classification factor, one significant function was developed and the percentage of correct classification was 84.92 %. The fatty acids C18-1cis9, C16:0, C4:0 and C10:0 contributed the most to discriminate milk samples according to breed and lactation stage.