Late-onset glutaric aciduria type II (GAII) is a rare but treatable cause of profound proximal myopathy. GAII is caused by defects in intra-mitochondrial acyl-CoA dehydrogenation due to deficiency in one of three molecules: the alpha or beta subunits of the electron transport flavoprotein (ETFA; OMIM 231680, ETFB; OMIM 130410), or ETF-dehydrogenase (ETFDH; OMIM 231675). This case report illustrates that GAII may present in the teenage years and may not be associated with hypoglycaemia. It outlines some important diagnostic conundrums faced in diagnosing and managing juvenile onset myopathies. Mutational analysis from this patient revealed two mutations of the ETF-DH gene: EFTDH-334C>T/His122Tyr and EFTDH-1366C>A/Pro456Thr (OMIM 231675). An outline of this rare but important disease, its clinical characteristics and diagnostic methodology are given.