The present study gives a detailed ultrastructural description of equine conceptuses at Day 14 (n = 2) and Day 16 (n = 3) after ovulation. Whereas on Day 14 only primitive structures were seen, on Day 16 neurulation and formation of mesodermal somites had taken place. The ectoderm of the embryo itself and the surrounding trophoblast ectodermal cells were characterised by specific cell surface differentiations. At the embryonic ectodermal cell surface (14 and 16 days) remarkable protruded and fused cytoplasmic projections were seen, typically associated with macropinocytotic events involved in macromolecule and fluid uptake. This finding adds an important point to the expansion mode of the hypotone equine conceptus, which is characterised by ‘uphill’ fluid uptake. Numerous microvilli and coated endocytotic pits at the apical trophoblast membrane emphasised its absorptive character. Endodermal cells were arranged loosely with only apically located cellular junctions leaving large intercellular compartments. At the border of the embryonic disc apoptotic cells were regularly observed indicating high remodelling activities in this area. Conspicuous blister-like structures between ectoderm and mesoderm were seen in the trilaminar part of Day-14 and -16 conceptuses. These were strictly circumscribed despite not being sealed by cellular junctions between germinal layers. It is possible that these blisters are involved in embryo positioning; however, further studies are needed to verify this.