The fine structure of human embryonic stem (ES) cell colonies was analysed by transmission electron microscopy (TEM) after 35 passages of in-vitro culture. Most cells formed compact, saucer-shaped colonies with epithelioid cells on the periphery and polygonal cells within the colony. Three morphological types of cells were identified based on their fine structure: undifferentiated cells resembling inner cell mass (ICM) cells of blastocysts; protein-synthesizing cells at the onset of cellular differentiation; and compact masses of secretory cells resembling unicellular goblet cells of the intestine. The predominant cell type was the undifferentiated ES cells resembling ICM cells of blastocysts. These cells had large nuclei containing reticulated nucleoli, well-developed rough endoplasmic reticulum (RER), Golgi complexes, elongated tubular mitochondria, lysosomes and typical centrosomes with centrioles associated with microtubules and microfilaments, organizing the cytoskeleton. Some ES cells have very large nuclei and scanty cytoplasms with fewer organelles. The isolated or attached protein-synthesizing cells at the onset of differentiation had extensive RER and large Golgi complexes. The morphologically differentiated cells formed compact colonies and resembled goblet-like cells in microstructure. They had RER and large Golgi complexes associated with secretory vesicles. The epithelioid cells at the periphery were columnar and largely polarized by centrosomes associated with Golgi complexes. Epithelioid cells in all three categories had specialized cell junctions (desmosomes), anchored by tonofilaments, and surface blebs. Isolated cells were seen on the surface, towards the centre of the colony, and their free surfaces had microvilli and larger blebs. Approximately 3-5% of all cells were mitotic, with typical bipolar spindles organized by centrosomes, pivotally located at the poles, and appeared to resemble typical somatic cells.