Density Functional Theory calculations have been used to investigate structural models for the ‘Very Rapid’ and ‘Inhibited’ EPR signals ascribed to xanthine oxidase Mo^V species. Analysis of the observed hyperfine coupling tensors has suggested close Mo–C contacts in both cases and a side-on interaction between the substrate’s carbonyl group and the Mo centre has been proposed. Attempts to confirm this for several model ‘Very Rapid’ species, based on a previous structure for the active site, either give short Mo–C contacts but too small a spin density on Mo or long Mo–C distances and a more reasonable Mo spin. Either the model system or the interpretation of the experimental data requires revision. In contrast, a good model can be developed for the ‘Inhibited’ species, which arises during reaction with formaldehyde, which is consistent with the EPR and other experimental data. However, rather than involving side-on co-ordination of the formaldehyde carbonyl group, the ‘Inhibited’ species forms a C–S bond between the formaldehyde and the sulfido ligand.