The Jahn–Teller effect is most often encountered in octahedral complexes of the transition metals.  The phenomenon is very common in six-coordinate copper(II) complexes. The d electronic configuration of this ion gives three electrons in the two degenerate e orbitals, leading to a doubly degenerate electronic ground state. Such complexes distort along one of the molecular fourfold axes (always labelled the z axis), which has the effect of removing the orbital and electronic degeneracies and lowering the overall energy. The distortion normally takes the form of elongating the bonds to the ligands lying along the z axis, but occasionally occurs as a shortening of these bonds instead (the Jahn–Teller theorem does not predict the direction of the distortion, only the presence of an unstable geometry). When such an elongation occurs, the effect is to lower the electrostatic repulsion between the electron-pair on the Lewis basic ligand and any electrons in orbitals with a z component, thus lowering the energy of the complex. The inversion centre is preserved after the distortion.
In octahedral complexes, the Jahn–Teller effect is most pronounced when an odd number of electrons occupy the e orbitals. This situation arises in complexes with the configurations d, low-spin d or high-spin d complexes, all of which have doubly degenerate ground states. In such compounds the e orbitals involved in the degeneracy point directly at the ligands, so distortion can result in a large energetic stabilisation. Strictly speaking, the effect also occurs when there is a degeneracy due to the electrons in the t orbitals (i.e. configurations such as d or d, both of which are triply degenerate). In such cases, however, the effect is much less noticeable, because there is a much smaller lowering of repulsion on taking ligands further away from the t orbitals, which do not point directly at the ligands (see the table below).  The same is true in tetrahedral complexes (e.g. manganate: distortion is very subtle because there is less stabilisation to be gained because the ligands are not pointing directly at the orbitals.
The expected effects for octahedral coordination are given in the following table:
w: weak Jahn–Teller effect (t orbitals unevenly occupied)
s: strong Jahn–Teller effect expected (e orbitals unevenly occupied)
blank: no Jahn–Teller effect expected.
The Jahn–Teller effect is manifested in the UV-VIS absorbance spectra of some compounds, where it often causes splitting of bands. It is readily apparent in the structures of many copper(II) complexes. Additional, detailed information about the anisotropy of such complexes and the nature of the ligand binding can be however obtained from the fine structure of the low-temperature electron spin resonance spectra.