The allocyclic X chromosome in early female mouse embryos undergoes DNA replication either late or early in the S phase. Earlier studies indicated that the early-replicating X chromosome is restricted to the trophectoderm and primitive endoderm cell lineages in which the allocyclic X is almost exclusively paternal in origin. There has been, however, no compelling evidence for the genetic inactivity of the early-replicating X chromosome and a shift from early to late replication or vice versa. The present study employing a combination of 3H-thymidine autoradiography and BrdU labeling-acridine orange fluorescence staining in day-6 female mouse embryos found that the early-replicating X chromosome can change directly into a late-replicating one. The activity state of the early-replicating X chromosome was examined by electrophoretic determination of the X linked enzyme, phosphoglycerate kinase (PGK-1), in tissues isolated from 6.0-day and day-8.5 Pgk-1a/Pgk-1b embryos. Only the maternally derived Pgk-1 allele was expressed in the proximal endoderm and extraembryonic ectoderm of 6.0-day and the chorion of 8.5-day embryos. Thus, the early-replicating, paternally derived X chromosome found in about 70%-80% of the cells in these tissues seems to be repressed like the late-replicating one.