Hematoxylin is a basic dye that gives a blue or blue-black color to acidic substances in cells and tissues. Thus the chromatin of the nuclei composed of desohyribonucleic acid is colored in dark blue by hematoxylin. In the same way, the cytoplasm is colored more or less intensely in blue due to the ribosomes which contain the ribonucleic acid. Substances or structures that stain blue with hematoxylin are called basophilic.

Hematoxylin is very commonly used in histology laboratories for routine staining. It is often associated with eosin to obtain a complete labeling of cellular structures.

There are now several hematoxylins called "modified":