Geographical position and feed quality of farms in highland and lowland, particularly in the tropical region, cause the differences in milk quality. One of the factors that influenced milk quality is the fatty acid (FA) profile of milk. The objective of this study is to compare the FA profiles of milk produced by farms in highland and lowland regions. Milk sampling was done by random purposive method at two regions which have different altitudes. Milk sampling was conducted with 28 farmers whose cows were fed botanically diverse forages and with commercial mix concentrate of dairy cows. The FA profiles of the milk samples were analyzed using Gas Chromatography (GC-7820A/G4350B, Agilent Technologies). Individual FAME was identified by comparison to standard mixture Supelco 37 Component FAME Mix and standard CLA (O5507, Sigma-Aldrich). The FA profiles were statistically analyzed for normality test and t-test carried out by SPSS ver.22. There were nine significantly different FA profiles consisting of C6:0, C10:0, C12:0, C14:0, C16:0, C18:0, C18:1-trans9, C18:2-trans, C18:2-cis, and C18:2-CLA. The milk from the lowland region has higher PUFA content, especially CLA content, and also has lower SFA content. The conclusion is milk from highland and lowland regions consists of different FA profiles.