True understanding of cell structure comes only from quantitative three-dimensional structural analysis. The term “structome”, coined by combining “structure” and “-ome”, is defined as quantitative three-dimensional structural information of whole cells at the electron microscopic level. I report here, for the first time, the structome of the cells of yeast Exophiala dermatitidis in the G1 phase determined using freeze-substitution and serial ultrathin sectioning electron microscopy. A typical E. dermatitidis G1-phase cell was ~4.9 μm in length, ~3.6 μm in diameter, and ~36 μm³ in volume. Its cell wall consisted of three layers and occupied 22% of the cell volume. Its nucleus was ~1.8 μm in diameter, and occupied ~7% of the cell volume. There was only one nucleolus, occupying ~16% of the nuclear volume. There were 17-52 mitochondria per cell, occupying 7-12% of the cell volume. Five to ten endoplasmic reticula were present in a cell, occupying ~0.2 % of the cell volume: they did not form a network in the cell. There were 1-4 vacuoles in a cell, occupying 4-10% of the cell volume. The Golgi apparatus, spindle pole body, autophagosomes, multi-vesicular bodies, lipid bodies, microtubules and microfilaments occupied ~1 % of the cell volume in total. About 200,000 ribosome particles and 1,000 glycogen granules were present per cell. The cytosol occupied 43-53 % of the cell volume. The membranes of cells of this yeast could be classified into three groups by their appearance and thickness.