beta(2)-Microglobulin, a small protein localized in serum and on cell surfaces, can adopt specific aggregating conformations that generate amyloid in tissues and joints as a complication to long-term hemodialysis. We characterize a proteolytic variant of beta(2)-microglobulin (cleaved after Lys(58)) that as a trimmed form (Lys(58) is removed) can be demonstrated in the circulation in patients with chronic disease. An unexpected electrophoretic heterogeneity of these two cleaved variants was demonstrated by capillary electrophoresis under physiological conditions. Each separated into a fast and a slow component while appearing homogeneous, except for a fraction of oxidized species detected by other techniques. The two components had different binding affinities for heparin and for the amyloid-specific dye Congo red, and the equilibrium between the two forms was dependent on solvent conditions. Together with analysis of the differences in circular dichroism, the results suggest that beta(2)-microglobulin cleaved after Lys(58) readily adopts two equilibrium conformations under native conditions. In the cleaved and trimmed beta(2)-microglobulin that appears in vivo, the less populated conformation is characterized by an increased affinity for Congo red. These observations may help elucidate why beta(2)-microglobulin polymerizes as amyloid in chronic hemodialysis and facilitate the search for means to inhibit this process.