Necdin is one of five genes associated with Prader-Willi syndrome, a rare genetic neurodevelopmental disease characterized by a variety of physical, cognitive, and behavioral defects. Necdin shows preferential paternal expression and belongs to the type II MAGE family. Necdin is a negative growth regulator, proposed to participate in a broad range of biological activities including cell growth, migration, differentiation and cell death/survival, but the precise molecular function is largely unknown. Here we report the sequence variation in cattle, sheep and goats, as well as its conservation in mammals. A gene fragment of 1,283 bp containing the entire coding region was amplified in 12 animals from different breeds in each of these 3 species, using conserved primers designed from cattle sequences. We found 1 intraspecies sequence variation in cattle and sheep and 2 in goat. Alternatively, we found differences at 7 positions between goat and sheep, 12 between goat and cattle and 16 between sheep and cattle. All the intraspecies variants were silent in the expected protein sequences but there were 3 amino acid changes between sheep and goat, 6 between goat and cattle and 9 between sheep and cattle. Only 3 of those changes were synonymous, and all the changes were found at the N-terminus. The phylogenetic relationship among these species and those of artiodactyla, carnivore, perisodactyla, primates, rodents, and proboscidea show very high sequence conservation, except for rodents and elephants. Due to its function, variation in necdin could have an effect on growth related traits in ruminants.