Cobalt and silver are toxic for cells, but mechanisms of this toxicity are largely unknown. Analysis of Corynebacterium glutamicum proteome from cells grown in control and cobalt or silver enriched media was performed by two dimensional gel electrophoresis (2DE) followed by mass spectrometry. Our results indicate that the cell adapted to cobalt stress by inducing five defense mechanisms: Scavenging of free radicals, promotion of the generation of energy, reparation of DNA, reparation and biogenesis of Fe-S cluster proteins and supporting and reparation of cell wall. In response to the detoxification of Ag+ many proteins were up-regulated, which involved reparation of damaged DNA, minimizing the toxic effect of reactive oxygen species (ROS) and energy generation. Overexpression of proteins involved in cell wall biosynthesis (1,4-alpha-glucan branching enzyme and nucleoside-diphosphate-sugar epimerase) upon cobalt stress and induction of proteins involved in energy metabolism (2-methylcitrate dehydratase and 1, 2-methylcitrate synthase) upon silver demonstrate the potential of these enzymes as biomarkers of sub-lethal Ag+ and Co toxicity.