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Zellweger syndrome (ZS), a fatal autosomal recessive disorder, is caused by defects in peroxisome biogenesis. Using a conditional knockout targeted to mouse brain, Müller et al. show that loss of PEX13, one of the genes mutated in ZS, recapitulates the symptoms of the disease, and results in mitochondrial-mediated oxidative stress, neuronal cell death and impaired cerebellar development. PEX13-deficient mice will be valuable for investigating the molecular basis and treatment of ZS cerebellar pathology.