This paper describes the use of capillary electrophoresis (CE) to examine the influence of different cations (C+; C+ = Na+ and tetra-n-alkylammonium, NR4 +, where R = Me, Et, Pr, Bu) on the rates of denaturation of bovine carbonic anhydrase II (BCA) in the presence of the anionic surfactant dodecylsulfate (DS−). Analysis of the denaturation of BCA in solutions of Na+DS− and NR4 +DS− (in Tris-Gly buffer) indicated that the rates of formation of complexes of denatured BCA with DS− (BCAD-DS−n,sat) are indistinguishable and independent of the cation below the critical micellar concentration (cmc), and independent of the total concentration of DS− above the cmc. At concentrations of C+DS− above the cmc, BCA denatured with rates that depended on the cation; the rates decreased by a factor > 104, in the order Na+ ~ NMe4 + > NEt4 + > NPr4 + > NBu4 + – the same order as the values of cmc (which decrease from 4.0 mM for Na+DS− to 0.9 mM for NBu4 +DS− in Tris-Gly buffer). The relationship between values of cmc and rates of formation of BCAD-DS−n,sat suggested that the kinetics of denaturation of BCA involve the association of this protein with monomeric DS−, rather than with micelles of (C+DS−)n. A less-detailed survey of seven other proteins (α-lactalbumin, β-lactoglobulin A, β-lactoglobulin B, carboxypeptidase B, creatine phosphokinase, myoglobin, and ubiquitin) showed that the difference between Na+DS− and NR4 +DS− observed with BCA was not general. Instead, the influence of NR4 + on the association of DS− with these proteins depended on the protein. The selection of cation contributed to the properties (including composition, electrophoretic mobility, and partitioning behavior in aqueous two-phase systems) of aggregates of denatured protein and DS−. These results suggest that variation in the behavior of NR4 +DS− with changes in R may be exploited in methods for analyzing and separating mixtures of proteins.