Although the diffusion of small molecules in amorphous polymers attracts much attention due to a variety of applications of polymer materials, little is known about the mechanism of diffusion. In this work, a new approach is developed for analyzing the diffusion of small molecules in glassy polymers. It is based on the concept that the transition-state free energies, F ‡ , of molecule jump from one sorption site to another are spatially correlated. The approach was used to analyze the experimental data of two diffusion-controlled reactions in glassy poly(ethyl methacrylate): deactivation of excited phenanthrene by oxygen and oxidation of p-phenylazophenyl nitrene. It has been found that, in the range from 90 to 155 K, the amplitude of spatial fluctuations of F ‡ increases linearly with temperature. The length of the spatial correlation of F ‡ does not depend on temperature; its value has been estimated to be about 1 nm. Based on these findings, we infer that the fluctuations of free energy F ‡ are caused by the heterogeneities of the localized vibrational modes in the polymer matrix.