AbstractThree‐dimensional domain swapping has been observed in increasing number of proteins and has been implicated in the initial stages of protein aggregation, including that of the cystatins. Stefin A folds as a monomer under native conditions, while under some denaturing conditions domain‐swapped dimer is formed. We have determined the backbone dynamics of the monomeric and domain‐swapped dimeric forms of stefin A by 15N relaxation using a model‐free approach. The overall correlation times of the molecules were determined to be 4.6 ± 0.1 ns and 9.2 ± 0.2 ns for the monomer and the dimer, respectively. In the monomer, decreased order parameters indicate an increased mobility for the N‐terminal trunk, the first and the second binding loops. At the opposite side of the molecule, the loop connecting the α‐helix with strand B, the beginning of strand B and the loop connecting strands C and D show increased localized mobility. In the domain‐swapped dimer, a distinctive feature of the structure is the concatenation of strands B and C into a single long β‐strand. The newly formed linker region between strands B and C, which substitutes for the first binding loop in the monomer, has order parameters typical for the remainder of the β‐strands. Thus, the interaction between subunits that occurs on domain‐swapping has consequences for the dynamics of the protein at long‐range from the site of conformational change, where an increased rigidity in the newly formed linker region is accompanied by an increased mobility of loops remote from that site. Proteins 2004. © 2004 Wiley‐Liss, Inc.