Gastrointestinal stromal tumors (GISTs) usually harbor activating mutations in KIT or PDGFRA, which promote tumorigenesis through activation of growth factor receptor signaling pathways. Around 15% of GISTs in adults and >90% in children lack such mutations ('wild-type' GISTs). Most gastric wild-type GISTs show loss of function of the Krebs cycle enzyme complex succinate dehydrogenase (SDH). However, the mechanism by which SDH deficiency drives tumorigenesis is unclear. Loss of SDH leads to succinate accumulation, which is thought to inhibit α-ketoglutarate-dependent dioxygenase enzymes, such as the TET family of DNA hydroxylases. TET proteins catalyze the conversion of 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC), which is required for subsequent DNA demethylation. Thus, TET-mediated 5-hmC production alters global DNA methylation patterns and may thereby influence gene expression. We investigated 5-hmC levels in a cohort of genotyped GISTs to determine whether loss of SDH was associated with inhibition of TET activity. 5-hmC levels were examined via immunohistochemistry in a cohort of 30 genotyped GISTs, including 10 SDH-deficient tumors (5 SDHA mutant; 1 SDHB mutant; 1 SDHC mutant; 3 unknown), 14 tumors with KIT mutations (10 in exon 11; 3 in exon 9; 1 in exon 17), and 6 tumors with PDGFRA mutations (all in exon 18). Staining for 5-hmC was negative in 9 of 10 (90%) SDH-deficient GISTs, 3 of 14 (21%) KIT-mutant GISTs, and 1 of 6 (17%) PDGFRA-mutant GISTs. The other SDH-deficient GIST showed weak staining for 5-hmC. Thus, 5-hmC was absent in nearly all SDH-deficient GISTs. These findings suggest that SDH deficiency may promote tumorigenesis through accumulation of succinate and inhibition of dioxygenase enzymes. Inhibition of TET activity may, in turn, alter global DNA methylation and gene expression in SDH-deficient tumors.