This study addresses the role of ATP-bound and free Mg2+ and Mn2+ ions in the activation and modulation of chaperonin-assisted refolding of urea-denatured malate dehydrogenase. As compared with Mg2+, Mn2+ ions caused a significant increase in the rate of GroE-assisted malate dehydrogenase refolding and, concomitantly, a decrease in the rate of ATP hydrolysis. Moreover, Mn2+ increases the affinity of GroES for GroEL, even in the presence of saturating amounts of Mg2+. Chemical cross-linking showed that lower concentrations of Mn-ATP as compared with Mg-ATP are needed to form both asymmetric GroEL14GroES7 and symmetric GroEL14(GroES7)2 particles. The manganese-dependent increase in the rate of protein folding concurred with a specific increase in the amount of symmetric GroEL14-(GroES7)2 particles detected in a chaperonin solution. Thus, Mn2+ is a cofactor that can markedly increase the efficiency of the chaperonin reaction in vitro. Mn2+ ions can serve as an important tool for analyzing the molecular mechanism and the structure of chaperonins.