Mitochondrial diseases are increasingly being recognized as causes of encephalopathy and intractable epilepsy. There is no gold-standard test for diagnosing mitochondrial disease, and the current diagnosis relies on establishing a consistent pattern of evidence from clinical data, neuroimaging, tissue biopsy, and biochemical, genetic, and other investigations. Experience in the diagnosis and treatment of patients with certain forms of mitochondrial disease, such as Alpers syndrome, is largely gained from case reports or small case series. The authors describe a case of Alpers syndrome due to POLG1 mutations, including serial neuroimaging and pathological investigations, to illustrate two main points: (1) Unique characteristics evident on serial diffusion-weighted imaging can be a valuable indicator of Alpers syndrome; and (2) abnormal lipid metabolism can be present in Alpers syndrome, which may need to be considered when using a ketogenic diet.