Zellweger syndrome is the prototypic human peroxisomal biogenesis disorder that results in abnormal neuronal migration in the central nervous system and severe neurologic dysfunction. A murine model for this disorder was previously developed by targeted deletion of the PEX2 peroxisomal gene. By labeling neuronal precursor cells in vivo with a mitotic marker, we can demonstrate a delay in neuronal migration in the cerebral cortex of homozygous PEX2 mutant mice. Postnatal PEX2 Zellweger mice develop severe cerebellar defects with abnormal Purkinje cell development and an altered folial pattern. When the PEX2 mutation is placed on an inbred murine genetic background, there is significant embryonic lethality and widespread neuronal lipidosis throughout the brain. Biochemical analysis of PEX2 mutant mice shows the characteristic accumulation of very long chain fatty acids and deficient plasmalogens in a wide variety of tissues. Docosahexaenoic acid levels (DHA; 22:6n-3) were found to be reduced in the brain of mutant mice but were normal in visceral organs at birth. All tissues examined in postnatal mutant mice had reduced DHA. The combined use of morphologic and biochemical analyses in these mice will be essential to elucidate the pathogenesis of this complex peroxisomal disease.