The effect of nutrition on milk fat yield and composition has largely been investigated in cows and goats, with some differences for fatty acid (FA) composition responses and marked species differences in milk fat yield response. Recently, the characterization of lipogenic genes in ruminant species allowed in vivo studies focused on the effect of nutrition on mammary expression of these genes, in cows (mainly fed milk fat-depressing diets) and goats (fed lipid-supplemented diets). These few studies demonstrated some similarities in the regulation of gene expression between the two species, although the responses were not always in agreement with milk FA secretion responses. A central role for trans-10 C18:1 and trans-10, cis-12 CLA as regulators of milk fat synthesis has been proposed. However, trans-10 C18:1 does not directly control milk fat synthesis in cows, despite the fact that it largely responds to dietary factors, with its concentration being negatively correlated with milk fat yield response in cows and, to a lesser extent, in goats. Milk trans-10, cis-12 CLA is often correlated with milk fat depression in cows but not in goats and, when postruminally infused, acts as an inhibitor of the expression of key lipogenic genes in cows. Recent evidence has also proven the inhibitory effect of the trans-9, cis-11 CLA isomer. The molecular mechanisms by which nutrients regulate lipogenic gene expression have yet to be well identified, but a central role for SREBP-1 has been outlined as mediator of FA effects, whereas the roles of PPARs and STAT5 need to be determined. It is expected that the development of in vitro functional systems for lipid synthesis and secretion will allow future progress toward (1) the identification of the inhibitors and activators of fat synthesis, (2) the knowledge of cellular mechanisms, and (3) the understanding of differences between ruminant species.