Initial cell lineages that presage the inner cell mass and extra-embryonic trophectoderm are established when eight blastomeres compact to form polarized morulae in preimplantation mouse development. FILIA has been identified as a binding partner to MATER (maternal antigen that embryos require; also known as NLRP5), which is encoded by a maternal effect gene. Products of each gene are detected in growing oocytes and, although transcripts are degraded before fertilization, the cognate proteins persist in early blastocysts. The two proteins co-localize to the cytocortex of ovulated eggs, where the stability of FILIA is dependent on the presence of MATER. After fertilization, FILIA-MATER complexes become asymmetrically restricted in the apical cytocortex of two-cell embryos due to their absence in regions of cell-cell contact. This asymmetry is reversible upon disaggregation of blastomeres of the two- and four-cell embryo. Each protein persists in cells of the preimplantation embryo, but the continuous cell-cell contact of ;inner' cells of the morulae seemingly precludes formation of the subcortical FILIA-MATER complex and results in cell populations that are marked by its presence (;outer') or absence (;inner'). Thus, the FILIA-MATER complex provides a molecular marker of embryonic cell lineages, but it remains to be determined if the molecular asymmetry established after the first cell division plays a role in cell fate determinations in the early mouse embryo. If so, the plasticity of the FILIA-MATER complex localization may reflect the regulative nature of preimplantation mouse development.