Schistosomes have lost the capability to synthesize fatty acids de novo, but they can modify fatty acids by chain elongation. This has a profound effect on the molecular species composition of the two main phospholipid fractions of schistosomes, phosphatidylcholine (PC) and phosphatidylethanolamine (PE). Molecular species of phospholipids are increasingly recognized as important mediators, or precursors thereof, in signal transduction, immune response modulation, and events like membrane fusion. As these are all important aspects of schistosome membranes and of the tegumental membranes in particular, we analysed the PE and PC molecular species of the tegumental membranes, the worm body and the blood of the host. With the aid of on-line mass spectrometry, we unequivocally identified a large number of PC and PE species in schistosomes, among which considerable amounts of plasmalogen species. This was unexpected, as this lipid subclass has been assumed to be absent in the parasite. Species, like (20:1-16:0) diacyl PC and (16:0-20:1) plasmalogen PE, found to be main constituents in schistosomes, were absent from the blood of the host. Large differences were also found between the molecular species composition of the tegumental membranes and the membranes of the worm body. In the tegumental membranes, 1-hexadecyl 2-palmitoyl PC was detected, which could possibly function as a precursor for platelet activating factor (PAF).