The nano-aluminosilicate mineral allophane is common in soils formed from parent materials containing volcanic ash and often contains Fe. Due to its lack of long-range order, the structure of allophane is still not completely understood. In the present study, Fe K-edge X-ray absorption fine structure (XAFS) was used to examine Fe-containing natural and synthetic allophane and imogolite samples. Results indicated that Fe substitutes for octahedrally coordinated Al in allophane, and that Fe exhibits a clustered distribution within the octahedral sheet. Iron adsorbed on allophane surfaces is characterized by spectral features distinct from those of isomorphically substituted Fe and of ferrihydrite. Fe adsorbed on the allophane surfaces probably exists as small polynuclear complexes exhibiting Fe–Fe edge sharing, similar to poorly crystalline Fe oxyhydroxides. The XAFS spectra of natural allophane and imogolite indicate that the Fe in the minerals is a combination of isomorphically substituted and surface-adsorbed Fe. In the synthetic Fe-substituted allophanes, the Fe XAFS spectra did not vary with the Al:Si ratio. Theoretical fits of the extended XAFS (EXAFS) spectra suggest that local atomic structure around octahedral Fe in allophanes is more similar to Fe in a smectite-like structure than to a published theoretical nanoball structure.