Thiopurines are among the most successful chemotherapeutic agents used for treating various human diseases, including acute lymphoblastic leukemia and chronic inflammation. Although metabolic conversion and the subsequent incorporation of 6-thioguanine ((S)G) nucleotides into nucleic acids are considered important for allowing the thiopurine drugs to induce their cytotoxic effects, alternative mechanisms may also exist. We hypothesized that an unbiased analysis of (S)G-induced perturbation of the entire proteome might uncover novel mechanism(s) of action of the drug. We performed a quantitative assessment of global protein expression in control and (S)G-treated Jurkat T cells by employing stable isotope labeling by amino acids in cell culture and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. LC-MS/MS quantification results uncovered substantially decreased expression of a large number of proteins in the mitochondrial respiratory chain complex, and Ingenuity Pathway Analysis of the significantly altered proteins showed that (S)G treatment induced mitochondrial dysfunction. This was accompanied by diminished uptake of MitoTracker Deep Red and the elevated formation of oxidatively induced DNA lesions, including 8,5'-cyclo-2'-deoxyadenosine and 8,5'-cyclo-2'-deoxyguanosine. Together, our results suggested that (S)G may exert its cytotoxic effect by inducing mitochondrial dysfunction and reactive oxygen species formation in acute lymphoblastic leukemia cells.