Iron-pyrite FeS represents the prototype compound of the crystallographic pyrite structure. The structure is cubic and was among the first crystal structures solved by X-ray diffraction. It belongs to the crystallographic space group Pa and is denoted by the Strukturbericht notation C2. Under thermodynamic standard conditions the lattice constant  of stoichiometric iron pyrite FeS amounts to . The unit cell is composed of a Fe face-centered cubic sublattice into which the  ions are embedded. (Note though that the iron atoms in the faces are not equivalent by translation alone to the iron atoms at the corners.) The pyrite structure is also seen in other MX compounds of transition metals M and chalcogens X = O, S, Se and Te. Certain dipnictides with X standing for P, As and Sb etc. are also known to adopt the pyrite structure.
The Fe atoms are bonded to six S atoms, giving a distorted octahedron. The material is a semiconductor. The Fe ions is usually considered to be low spin divalent state (as shown by Mössbauer spectroscopy as well as XPS). The material as a whole behaves as a Van Vleck paramagnet, despite its low-spin divalency.
The sulfur centers occur in pairs, described as S..  This material features ferric ions and isolated sulfide (S) centers.
The S atoms are tetrahedral, being bonded to three Fe centers and one other S atom. The site symmetry at Fe and S positions is accounted for by point symmetry groups C and C, respectively. The missing center of inversion at S lattice sites has important consequences for the crystallographic and physical properties of iron pyrite. These consequences derive from the crystal electric field active at the sulfur lattice site, which causes a polarization of S ions in the pyrite lattice. The polarisation can be calculated on the basis of higher-order Madelung constants and has to be included in the calculation of the lattice energy by using a generalised Born–Haber cycle. This reflects the fact that the covalent bond in the sulfur pair is inadequately accounted for by a strictly ionic treatment.
Arsenopyrite has a related structure with heteroatomic As–S pairs rather than S-S pairs. Marcasite also possesses homoatomic anion pairs, but the arrangement of the metal and diatomic anions differ from that of pyrite. Despite its name, chalcopyrite () does not contain dianion pairs, but single S sulfide anions.