There is a predominant theory for the evolution of the mammalian Y chromosome. This theory hypothesizes that genes for sex determination and male-specific traits, as well as sequences for X-Y meiotic pairing, are conserved on the mammalian Y chromosome across all lineages and that all other Y chromosomal genes or sequences have been or will be lost in each mammalian lineage. There are effects of mouse Y chromosomal genes on behaviors and other traits that are not male specific. Under the predominant theory, these Y chromosomal genes could be the same as the conserved genes for sex determination or male-specific traits, or they could be genes that have been lost from the Y chromosomes of other mammalian lineages and that will eventually be lost from the Y chromosome of the rodent lineage. Recently, the evolution of the primate and rodent Y chromosomes has been studied at the DNA level. These studies are summarized and reviewed in this article. The findings of these studies are not fully consistent with the predominant theory for the evolution of the mammalian Y chromosome. Also, they imply that there are other possibilities for the phylogenetic history of Y chromosomal genes of mice with effects on behavior. These are that Y chromosomal genes with effects on mouse behaviors or other traits could be conserved genes other than those for sex determination or male-specific traits or that they could be novel genes on the Y chromosome of the rodent or Mus lineage.