Zeolites containing transition-metal ions (TMIs) often show promising activity as heterogeneous catalysts in pollution abatement and selective oxidation reactions. In this paper, two aspects of research on the TMIs Cu, Co, and Fe in zeolites are discussed: (i) coordination to the lattice and (ii) activated oxygen species. At low loading, TMIs preferably occupy exchange sites in six-membered oxygen rings (6MR), where the TMIs preferentially coordinate with the O atoms of Al tetrahedra. High TMI loadings result in a variety of TMI species formed at the zeolite surface. Removal of the extralattice O atoms during high-temperature pretreatments can result in autoreduction. Oxidation of reduced TMI sites often results in the formation of highly reactive oxygen species. In Cu-ZSM-5, calcination with O-2 results in the formation of a species, which was found to be a crucial intermediate in both the direct decomposition of NO and N2O and the selective oxidation of methane into methanol. An activated oxygen species, called alpha-O, is formed in Fe-ZSM5 and reported to be the active site in the partial oxidation of methane and benzene into methanol and phenol, respectively. However, this reactive alpha-O can only be formed with N2O, not with O-2. O-2-activated Co intermediates in faujasite (FAU) zeolites can selectively oxidize a-pinene and epoxidize styrene. In Co-FAU, Co-III superoxo and peroxo complexes are suggested to be the active cores, whereas in Cu and Fe-ZSM-5, various monomeric and dimeric sites have been proposed, but no consensus has been obtained. Very recently, the active site in Cu-ZSM-5 was identified as a bent [Cu-O-Cu](2+) core (Proc. Natl. Acad. Sci. U.S.A. 2009, 106,18908-18913). Overall, O-2 activation depends on the interplay of structural factors such as the type of zeolite and sizes of the channels and cages and chemical factors such as the Si/Al ratio and the nature, charge, and distribution of the charge-balancing cations. The presence of several different TMI sites hinders the direct study of the spectroscopic features of the active site. Spectroscopic techniques capable of selectively probing these sites, even if they only constitute a minor fraction of the total amount of TMI sites, are thus required. Fundamental knowledge of the geometric and electronic structures of the reactive active site can help in the design of novel selective oxidation catalysts.