Pregnancy losses are substantial in dairy cattle and threaten reproductive efficiency. A significant portion of these losses occur during early stages of conceptus development, including the elongation phase. Elongation is a prerequisite for maternal recognition, implantation, and survival of pregnancy, and entails remarkable expansion of extraembryonic tissues along the uterine lumen in a short window of development. In a process not fully understood, the uterine histotroph increases the rate of proliferation and migration of conceptus cells and drives elongation. Using microarray technology, our research group investigated the transcriptome of bovine conceptus cells at early stages of elongation. The results demonstrated remarkable changes in biology of conceptus cells at the onset of elongation, which seem to characterize a cellular reprogramming event required for successful elongation. Functional analyses of the data revealed that substantial part of these changes are related to the metabolism of conceptus cells and, more specifically, indicated a greater utilization of lipids for synthesis of biomass, energy, cell signaling, and regulation of gene expression. Using liquid chromatography and mass spectroscopy, we investigated the composition of the histotroph and observed that lipids are in fact a constitutive part of the histotroph at the onset of elongation. Moreover, important differences in the histotroph composition were observed between pregnant and nonpregnant cows. These high-throughput platforms were also used to compare conceptuses and histotroph among groups of cows with distinct differences fertility to identify potential deviations from the norm that might be causing early pregnancy losses. We are now investigating the detailed composition of fatty acids and derivatives in the histotroph throughout the estrous cycle and early pregnancy, searching for SNPs located within regulatory regions of candidate genes believed to be important for elongation, and investigating their association with fertility traits in dairy cattle. Our long-term goal is not only to unravel the biology of conceptus elongation but also to develop strategies to minimize pregnancy losses in dairy cows.