Intracellular structures in Pichia pastoris can be visualized by the complementary methods of fluorescence microscopy and electron microscopy. An improved immunofluorescence protocol yields better optics and more reliable antigen preservation than conventional methods. As an alternative to immunofluorescence, if a protein of interest is fused to GFP or another fluorescent tag, the cells can be fixed and viewed directly. For higher-resolution studies of organelle morphology, thin-section electron microscopy of permanganate-fixed cells yields good preservation of intracellular membranes.