Germline mutations in the genes encoding the B (SDHB) and D (SDHD) subunits of the heterotetrameric protein succinate dehydrogenase (mitochondrial complex II) are important causes of inherited and apparently sporadic paragangliomas. In an effort to further investigate the role of these genes in malignant sympathetic paragangliomas and adrenal pheochromocytomas, we screened a series of tumors for mutations in SDHB and SDHD. Mutation testing was performed on DNA extracted from formalin-fixed, paraffin-embedded tumors and associated normal tissues by polymerase chain reaction amplification and direct sequencing of the coding regions and intron-exon junctions of the SDHB and SDHD genes. Among 16 malignant paragangliomas with proven metastases, 6 (38%) had mutations in SDHB (2 nonsense, 1 splice site, 1 insertion causing a frameshift, and 2 presumably deleterious missense mutations). Probable deleterious SDHB variants were also detected in 5 (45%) of 11 paragangliomas without known metastatic disease (1 splice site, 1 deletion causing a frameshift, and 3 missense changes). In 12 malignant pheochromocytomas, 1 SDHD and no SDHB mutations were identified. The identical SDHB mutation was detected in DNA extracted from accompanying normal tissue for each of the 10 cases on which this analysis was performed. An excess of SDHB mutations in paragangliomas versus pheochromocytomas was found, with no difference in the frequency of mutations in malignant versus benign paragangliomas. The disparate mutational spectra in malignant paragangliomas and pheochromocytomas may reflect differences in underlying tumor biology.