Pregnancy is a complex physiological process relying on precise coordination of molecular events which are crucial to the well-being of both the mother and the developing fetus. Uterine dysfunction can have critical implications for fetal development, with an estimated 75% of failed pregnancies attributed to implantation defects (Cheng et al., 2023). ATP11A, a phospholipid flippase, has been identified to play a key role in placental function, ultimately leading to fetal heart developmental defects in knockout (KO) mouse embryos. It was even observed that >30% of wildtype pups presented with heart development defects when their mother was heterozygous for the Atp11a gene (Radford et al., 2023). The current project investigates the molecular consequences of Atp11a gene loss in uterine function. During my project, I corroborated a profound sub-fertility phenotype in Atp11a+/-females. I then assessed uterine functionality in Atp11a KO females (generated through placental rescue) using bulk RNA-sequencing and a series of histological analyses. RNA-sequencing data from uterine samples indicated that the uterine epithelial layer is most sensitive to the loss of Atp11a. Furthermore, samples staged closer to E4.0 were more greatly impacted by the loss of Atp11a compared to samples staged E3.5, identifying a critical window during the peri-implantation period during which ATP11A is of great importance. In addition, immunofluorescence staining results from Atp11a KO females demonstrated that various defects are present in the luminal epithelium of the uterus, the site of embryo implantation, ranging from a disorganized morphology of the columnar epithelium to the mis-expression of key transcription factors and hormone receptors. Moreover, I found a stark reduction in staining intensity of SOX9 in the uterine glands, a marker of epithelial progenitor cells that help replenish both the glandular and luminal epithelium. These data implicate the epithelial compartment as a key culprit for the reduced reproductive success of Atp11a-depleted females. Moreover, RNA-sequencing data from placental samples showed that Atp11a heterozygosity in the uterus-derived maternal part of the placenta even has a profound impact on the transcriptome of placental trophoblast. No parent-of-origin or sex specific effects were evident. Taken together, my findings indicate that Atp11a deficiency causes uterine dysfunction, specifically affecting the epithelium which is, importantly, the site of implantation. These perturbations are most profound at E4.0, which is the beginning of the narrow window of receptivity. As a result, this may lead to early implantation failure, thus explaining the sub-fertility phenotype that is observed even in heterozygous females. In milder cases where pregnancy is established, Atp11a function in uterine glandular epithelial cells may lead to an abnormal development of the placenta that, in turn, likely underlies the increased incidence of fetal congenital heart defects. My data will help to gain a better understanding of the causes of infertility as well as idiopathic congenital heart defects, with a long-term prospect of discovering targeted interventions to mitigate such developmental defects in pregnancy.