A series of events during the first four days of mouse embryo development leads to the formation of a blastocyst. The blastocyst consists of neatly segregated three lineages: the epiblast (EPI), which will form the fetus, the extra-embryonic primitive endoderm and the outer layer of the extra-embryonic trophectoderm (TE). This organization prepares the embryo for implantation and subsequent development. This study aims to explore two broad questions: 1) what mechanisms dictate the fate of the progenies of the chromosomally abnormal cells generated during the 4-8 cell stage division; 2) how the transcriptional heterogeneities between the blastomeres of the 4-cell stage embryo affect subsequent lineage segregation. A high incidence of aneuploidy in the early cleavage divisions is considered the principal cause for low human fecundity and developmental defects. However, there is a dramatic decline in the prevalence of aneuploidy as gestation progresses. To understand the fate of aneuploid cells, a mouse model of chromosome mosaicism was used. In vitro culture system and live imaging demonstrated that aneuploid cells were eliminated from the EPI by apoptosis both during pre- and peri-implantation development. Also, aneuploid cells displayed chronic proteotoxic stress. Subsequently, p53-mediated autophagy eliminated aneuploid cells from the EPI. Unlike aneuploid embryos, 1:1 diploid-aneuploid mosaic embryos show developmental potential equivalent to diploids. Their peri-implantation development was followed, and it was found that while aneuploid cells in the EPI underwent apoptosis, the diploid cells over-proliferated to regulate the overall EPI size. These results elucidate the cellular and molecular mechanisms used by mouse embryo to refine the EPI cell population and ensure only the chromosomally fit cells proceed through the development of the fetus. The second part of the study investigates into the early molecular players that bias cell fate decisions. Sox21 was earlier identified as the most heterogeneous gene at the 4-cell stage that can influence cell fate decision. The deep sequencing of Sox21 knockout and wild-type embryos was carried out at the 4-cell stage and compared. Klf2 and Tdgf1 were found to be important downstream targets of Sox21 that influence lineage segregation. Depletion of both these genes predisposed cells to the TE lineage. Co-overexpression of both these genes rescued the effect of Sox21 knockdown on cell fate. These results demonstrate the mechanism by which Sox21 heterogeneity, from as early as the 4-cell stage, biases cell fate. Together, these findings indicate the fundamental mechanisms used by mouse embryo to ensure developmental plasticity.