The first lineage segregation in the pre-implantation mouse embryo gives rise to cells of the inner cell mass and the trophectoderm. Segregation into these two lineages during the 8-cell to 32-cell stages is accompanied by a significant amount of cell displacement, and as such it has been difficult to accurately track cellular behavior using conventional imaging techniques. Consequently, how cellular behaviors correlate with cell fate choices is still not fully understood. To achieve the high spatial and temporal resolution necessary for tracking individual cell lineages, we utilized two-photon light-scanning microscopy (TPLSM) to visualize and follow every cell in the embryo using fluorescent markers. We found that cells undergoing asymmetric cell fate divisions originate from a unique population of cells that have been previously classified as either outer or inner cells. This imaging technique coupled with a tracking algorithm we developed allows us to show that these cells, which we refer to as intermediate cells, share features of inner cells but exhibit different dynamic behaviors and a tendency to expose their cell surface in the mouse embryo between the fourth and fifth cleavages. We provide an accurate description of the correlation between cell division order and cell fate, and demonstrate that cell cleavage angle is a more accurate indicator of cellular polarity than cell fate. Our studies demonstrate the utility of two-photon imaging in answering questions in the pre-implantation field that have previously been difficult or impossible to address. Our studies provide a framework for the future use of specific markers to track cell fate molecularly and with high accuracy.