Dystonias are a clinically and genetically heterogeneous group of movement disorders characterized by involuntary, sustained muscular contractions affecting one or more sites of the body, and abnormal postures. In this study, we describe an autosomal recessive family that presents with a progressive and early-onset form of generalized dystonia. The nuclear family consists of two healthy parents and two affected daughters. To elucidate the genetic causes underlying disease, whole-exome sequencing analysis was performed in one affected sibling, followed by validation, biochemical analyses and MRI brain imaging. A homozygous, disease-segregating mutation (p.Val400Met) was identified in the glutaryl-CoA dehydrogenase (GCDH) gene at chromosome 19p13. The mutation, in an amino acid that is highly conserved among species, was absent in large number of neurologically normal individuals. Biochemical analyses demonstrated increased 3-hydroxy glutaric acid present in urine samples from both patients. MRI imaging revealed a T2 and flair hyperintense signal in lenticular nuclei with bilateral and symmetrical distribution. We conclude that both GCDH activity and GCDH mutation analysis should be considered in the differential diagnosis of progressive forms of early-onset generalized dystonia and that mitochondrial fatty acid metabolism is one important pathway in the development of dystonia. As lysine restriction and L: -carnitine supplementation are important treatments for GCDH deficiency, identification of this deficiency in patients with progressive forms of early-onset generalized dystonia has potential treatment implications.