Chromatin remodeling by histone and DNA modification is important for the initiation of X-chromosome inactivation (XCI). In this study, a thorough transcriptional analysis of five XCI-related genes was performed by single cell reverse-transcribed PCR. An analysis of the XCI-related gene (Xist, Tsix, SUV39H1, SET7, and DNMT1) expression was performed to investigate the initiation process of XCI from early mouse single embryo (1-cell, 2-cell, 4-cell, 8-cell, and blastocyst). Detection of the expression of Xist and Tsix from single 2-cell embryo was feasible, although the expression of those genes was very low in single 1-cell embryo. Transcription of those genes may be activated from single 2-cell embryo. After determining the sex of single embryo by Y-chromosome-specific Zfy expression, we found that Tsix could be detected from both male and female single embryos, but it was only possible to detect Xist from female single embryo. XCI chromatin-remodeling genes, such as histone H3 methylation enzymes (SUV39H1 and SET7) and DNA methylation enzyme (DNMT1), were expressed during all early phases of embryogenesis. The expression of those genes in single embryo was not dependent on sex. Our study illustrated that the expression of these chromatin-remodeling genes, SUV39H1, DNMT1, and SET7, may be originated from germ cells, which were not dependent on zygotic activation of Xist from female single embryo.