The fine structure of mouse embryonic stem (ES) cell colonies was analysed by scanning and transmission electron microscopy. Most of the ES cells had numerous microvilli of different lengths. Coated pits and vesicles were also seen along areas of the peripheral cytoplasm and plasma membranes. Junctional complexes including gap junctions were observed between adjacent ES cells. These cells had Golgi complexes, spherical to oval mitochondria, lysosomes and typical centrioles, microfilaments and microtubules and large nuclei containing reticulated nucleoli. These results are consistent with the ultrastructural features of undifferentiated cells.