Hematoxylin and eosin (H&E) staining is the most fundamental technique in histopathology. It is the first stain applied to virtually every tissue sample submitted for diagnostic analysis, and it remains the primary method pathologists use to assess tissue architecture and cell morphology.
H&E uses two dyes applied in sequence. Hematoxylin binds to nucleic acids in the cell nucleus, staining it blue/purple. Because every cell has a nucleus, hematoxylin gives the pathologist a complete picture of cell distribution and density across the tissue. Eosin binds to proteins in the cytoplasm and extracellular matrix, staining them pink. This reveals the structure of the cell body and the surrounding connective tissue.
Together, these two stains reveal tissue architecture, showing how cells are organized, how densely they are packed, and whether that organization looks normal or abnormal.
On a well-prepared H&E slide, a pathologist can identify cell morphology including the size, shape, and appearance of individual cells. Nuclear features such as enlarged nuclei, irregular nuclear borders, and high nuclear-to-cytoplasmic ratio are all associated with malignancy. The pathologist can also assess tissue architecture, tumor boundaries, and stromal components including connective tissue, vasculature, and immune infiltrates surrounding the tumor.
H&E reveals structure and morphology, but it cannot tell a pathologist which specific proteins a cell is expressing. Two tumors that look similar on H&E may have completely different molecular profiles and therefore require different treatments. This is why IHC is used alongside H&E. H&E establishes what the tissue looks like, and IHC establishes what proteins it is expressing.