The structural and magnetic properties of nanocrystalline manganese, cobalt, and nickel spinel ferrites dispersed in a highly porous SiO2 aerogel matrix were studied. X-ray diffraction and high-resolution transmission electron microscopy indicate that single crystalline ferrite nanoparticles are well dispersed in the amorphous matrix. The cation distribution between the octahedral and tetrahedral sites of the spinel structure was investigated by X-ray absorption spectroscopy. The analysis of both the X-ray absorption near edge structure and the extended X-ray absorption fine structure indicates that the degree of inversion of the spinel structure increases in the series Mn, Co, and Ni spinel, in accordance with the values commonly found in the corresponding bulk spinels. In particular, fitting of the EXAFS data indicates that the degree of inversion in nanosized ferrites is 0.20 for MnFe2O4, 0.68 for CoFe2O4, and 1.00 for NiFe2O4. Magnetic characterization further supports these findings.