The Zellweger syndrome is a lethal hereditary disease characterized by the absence of peroxisomes (microbodies) in liver and kidney, and variable abnormalities in mitochondria. We show here that tissues from five infants that had died of this syndrome contain less than 10% of the normal levels of phosphatidylethanolamine plasmalogen (pPE), a major phospholipid component of cellular membranes. Heart and muscle, but not other tissues, also contain a substantial fraction of phosphatidylcholine plasmalogen (pPC), and this fraction is also strongly reduced in the Zellweger patients. No other abnormalities in cellular phospholipids were detected. Key enzymes of the biosynthesis of plasmalogens have previously been shown to be exclusively located in the peroxisomes of rodent liver and the microperoxisomes of rodent brain. We infer that the corresponding enzymes are also located in peroxisomes in man and that the absence of peroxisomes in Zellweger patients leads to their inability to synthesize plasmalogens. Our results support the notion that the biosynthetic role of peroxisomes in mammals has thus far been underestimated. We suggest that the defect in plasmalogen synthesis and possibly as yet unknown peroxisomal reactions are responsible for the diverse abnormalities observed in Zellweger patients.