Germ cells, after fate determination as primordial germ cells (PGCs) in early embryos, undergo various unique changes in epigenetic status during their development, and these changes differ from the epigenetic changes occurring in any other somatic cells. For example, PGCs undergo demethylation of DNA and change histone modification states on a genome-wide scale. Although the full physiological significance of these epigenetic alterations is still unclear, we can now discuss some of their mechanisms due to recent experimental evidence demonstrating the expression of candidate molecules involved in the processes of epigenetic change. On the other hand, DNA demethylation associated with PGC-specific gene expression, reprogramming of imprinted genes and regulation of retrotransposons in PGCs differentially occur from the genome-wide DNA demethylation. The tendency of epigenetic changes to appear on the whole genome, as well as more precise changes in the epigenetic status of particular parts of the genome, may play important roles in establishing the properties of PGCs required for acquiring totipotency.