Genome-wide changes of DNA methylation by active and passive demethylation processes are typical features during preimplantation development. Here we provide an insight that epigenetic reprogramming of DNA methylation is regulated in a region-specific manner, not a genome-wide fashion. To address this hypothesis, methylation states of three repetitive genomic regions were monitored at various developmental stages in the mouse embryos. Active demethylation was not observed in the IAP sequences whereas methylation reprogramming of the satellite sequences was regulated only by the active mechanism. Etn elements were actively demethylated after fertilization, passively demethylated by the 8-cell stage, and de novo methylated at the morular and blastocyst stages, showing dynamic epigenetic changes. Thus, our findings suggest that the specific genomic regions or sequences may spatially/temporally have their unique characteristics in the reprogramming of the DNA methylation during preimplantation development.