Background: Succinate dehydrogenase assembly factors (SDHAF1-4) have been identified as playing a crucial role in the maturation of individual SDH subunits and assembly of the functioning SDH complex as a whole. Methods and Results: Through the use of massively parallel sequencing, we identified a variant in SDH assembly factor 3 (SDHAF3), c.157T>C (p.Phe53Leu), which was associated with increased prevalence in familial and sporadic pheochromocytoma and/or paraganglioma (6.6%) when compared to normal populations (1.2% [1000 Genomes], p=0.003; 2.1% [Exome Aggregation Consortium], p=0.0063). As this variant was deemed “probably damaging” to protein function (using in silico prediction tools [PolyPhen2, SIFT]), we explored the functional consequences of the resulting amino acid change (p.Phe53Leu) in both yeast and human cells. In yeast, introduction of the SDHAF3 variant (p.Phe53Leu) into Sdh7 null yeast (ortholog of SDHAF3 in humans) resulted in impaired function, as observed by its failure to restore SDH activity when expressed in Sdh7 null yeast relative to WT SDHAF3. As SDHAF3 is involved in maturation of SDHB, we tested the functional impact of SDHAF3 c.157T>C and various clinically relevant SDHB mutations on this interaction. Our in vitro studies in human cells show that SDHAF3 interacts with SDHB (residues 46 and 242), with impaired interaction observed in the presence of the SDHAF3 c.157T>C variant. Conclusions: Our studies reveal novel insights into the biogenesis of SDH, uncovering a vital interaction between SDHAF3 and SDHB. We have shown that SDHAF3 interacts directly with SDHB (residue 242 being key to this interaction), and that a variant in SDHAF3 (c.157T>C [p.Phe53Leu]) may be more prevalent in individuals with pheochromocytoma and/or paraganglioma, and is hypomorphic via impaired interaction with SDHB.