Hematoxylin staining is a well-established technique in histopathology and cytology for the diagnosis of malignant and non-malignant lesions. This compound forms strongly colored complexes with Fe(III) and Al(III) salts. Hematoxylin can be used as a primary stain and as a counterstain where it will differentiate acidophilic materials from basophilic materials and stain non-cellular substances such as fibrin, crystals, and pigments in various shades depending on the nature of the mordant used and the second stain.

Anthraquinone has yet to be found in nature. Of all the quinones found naturally, those derived from anthraquinone far exceed all others. Many of these are found in molds. Derivatives of 9,10-anthracenedione (anthraquinones) with several hydroxy and other functional groups are biologically active compounds isolated from Rubia and Cassia medical plant species. Anthraquinone is a comparatively safe compound: LD50 (rat) is 3500 mg/kg. It is a mild allergen and, as a fine powder, may cause skin irritation. Exposure to 3,000 ppm may be tolerated for only 30–60 min after which irritation of the nose, throat, and lungs may occur along with headaches, dizziness, and slurred speech. 9,10-anthraquinone is a weak carcinogen. Aside from its major use in the manufacture of intermediates for anthraquinone dyes and pigments, anthraquinone is finding increasing interest as a catalyst in the pulping of wood, in the polymerization of various materials for plastics, and in the isomerization of vegetable oils. It has been used to make seeds distasteful to birds (bird repellent) and as an accelerator in nickel electroplating.