Background: The myopathic form of carnitine palmitoyltransferase type II deficiency is an inherited autosomal recessive metabolic myopathy usually starting in childhood. Most reports have been on European and Japanese populations, and no Native South American patients have been reported to date. The p.Ser113Leu mutation is the most frequent in the European population. Only lower-leg magnetic resonance imaging findings have been reported, with gluteus maximus involvement in one case and normal imaging in other patients. Case presentation: Two Native South American siblings, a boy and a girl, presented to our neuromuscular clinic with recurrent rhabdomyolysis associated with transient muscle weakness after prolonged exercise. During episodes, their creatine kinase concentrations were markedly increased, up to 148,000 (1.48 × 10 5 ) IU/L in the boy and 18,000 (1.8 × 10 4 ) IU/L in the girl. The results of electroneuromyography and histopathology suggested a nonspecific myopathy. CPT2 gene sequencing showed two heterozygous mutations: the p.Ser113Leu variant and a novel one (predicted to be deleterious by in silico analysis), the p.Ser373Pro variant. The patients' parents were asymptomatic carriers. Whole-body magnetic resonance imaging showed mild selective involvement in the thoracic extensors and pelvic girdle in both siblings, and in the thighs and lower legs in one of them. Dietary and bezafibrate treatment was started, and symptomatic relief was observed. Conclusions: To the best of our knowledge, this is the first reported Native South American family with a CPT2 deficiency carrying a novel mutation and particular features visualized by whole-body magnetic resonance imaging.