In two patients who presented at late infancy with hypotonia, nystagmus and ataxia, interspersed with acute episodes of encephalopathy, we identified a mutation in a complex I assembly factor, NDUFA12L, which resulted in a marked reduction of the NDUFA12L protein and of complex I activity. The involvement of the mamillothalamic tracts, substantia nigra/medial lemniscus, medial longitudinal fasciculus, the corpus medullare and the cerebellum, with relative sparing of the cortex and subcortical white matter was distinctive and resembled the findings in the first and only known patient with mutation in the NDUFA12L gene.