The structural parameters, i.e., coordination numbers, bond distances and disorder obtained from the analysis of EXAFS spectra may sometimes be significantly influenced by errors introduced due to the inadequacy of the analysis method applied. Especially in the case of heterogeneous catalysts it has been realized that often there is a need to use an improved EXAFS data analysis compared to the simple harmonic approach which works well for well-defined bulk structures. This is due to the fact that catalysts contain highly dispersed or disordered structures with pair distribution functions quite different from well-crystalline bulk materials. In addition, the increased interest for in situ studies, which typically imply high temperatures, makes the influence from anharmonic vibrations on the shape of the pair distribution a significant factor. In this paper, we discuss the importance of asymmetric pair distribution functions for nano-sized particles and how they influence the structural parameters obtained from the standard data analysis. An alternative method, which takes into account deviations from the Gaussian pair distribution function typically used in the analysis of EXAFS spectra, will be described. The method is based on an analysis of the pair distribution functions derived from molecular dynamics simulations of small metal particles and its reliability is demonstrated by comparing structural parameters obtained from independent X-ray diffraction experiments.