Nanoparticle assemblies (NPAs) have emerged as a new way of designing novel materials since their optical, mechanical, electric and magnetic properties can be strongly modified. It has been shown that the spatial arrangement of constituent nanoparticles in the assembly, i.e., the NPA structure, plays an important role for the overall properties, but the tools for characterizing this are inadequate. In this work we developed the sasPDF method, which extends the atomic PDF analysis to the study of x-ray small angle scattering (SAS) data and applied it to study a variety of NPA structures. The method is demonstrated on NPA samples with different levels of structural order and yields quantitative information about details of the structure such as the local packing of particles in the NPA structure. Finally, we developed and have released, PDFgetS3, a program for extracting the pair distribution function from the SAS data.