Multidomain proteins in which consecutive globular regions are connected by linkers are prevalent in nature (Levitt in Proc Natl Acad Sci USA 106:11079-11084, 2009). Some members of this family have largely resisted structural characterization as a result of challenges associated with their inherent flexibility. Small-angle scattering (SAS) is often the method of choice for their structural study. An extensive set of simulated data for both flexible and rigid multidomain systems was analyzed and modeled using standard protocols. This study clearly shows that SAXS profiles obtained from highly flexible proteins can be wrongly interpreted as arising from a rigid structure. In this context, it would be important to identify features from the SAXS data or from the derived structural models that indicate interdomain motions to differentiate between these two scenarios. Features of SAXS data that identify flexible proteins are: (1) general attenuation of fine structure in the scattering profiles, which becomes more dramatic in Kratky representations, and (2) a reduced number of interdomain correlation peaks in p(r) functions that also present large D (max) values and a smooth decrease to 0. When modeling this dynamically averaged SAXS data, the structures obtained present characteristic trends: (1) ab initio models display a decrease in resolution, and (2) rigid-body models present highly extended conformations with a lack of interdomain contacts. The ensemble optimization method represents an excellent strategy to identify interdomain motions unambiguously. This study provides information that should help researchers to select the best modeling strategy for the structural interpretation of SAS experiments of multidomain proteins.