The structure and chemical differences among amorphous, crystalline and nanocrystalline molybdenum oxide aerogels were determined using extended X-ray absorption fine structure (EXAFS), Fourier transform infrared (FTIR) analysis and powder X-ray diffraction (XRD). These different forms of the same nominal material are produced by heat treatment. The influence of the structural differences on electrochemical properties was examined using stepped cyclic voltammetry. The most interesting material was the MoO3 aerogel heated to 300 degreesC. The material was found to be nanocrystalline; there are no XRD peaks but the EXAFS were virtually identical to orthorhombic MoO3. The electrochemcial response of the nanocrystalline material contains characteristics of both the amorphous and crystalline forms, but with better lithium capacity than either one.