β-Hematin crystals are made of dimers of hematin molecules that are, in turn, joined together by hydrogen bonds to form larger structures. In these dimers, an iron-oxygen coordinate bond links the central iron of one hematin to the oxygen of the carboxylate side-chain of the adjacent hematin. These reciprocal iron–oxygen bonds are highly unusual and have not been observed in any other porphyrin dimer. β-Hematin can be either a cyclic dimer or a linear polymer, a polymeric form has never been found in hemozoin, disproving the widely held idea that hemozoin is produced by the enzyme heme-polymerase.
Hemozoin crystals have a distinct triclinic structure and are weakly magnetic. The difference between diamagnetic low-spin oxyhemoglobin and paramagnetic hemozoin can be used for isolation. They also exhibit optical dichroism, meaning they absorb light more strongly along their length than across their width, enabling the automated detection of malaria. Hemozoin is produced in a form that, under the action of an applied magnetic field, gives rise to an induced optical dichroism characteristic of the hemozoin concentration; and precise measurement of this induced dichroism (Magnetic circular dichroism) may be used to determine the level of malarial infection.