Sheared flagella from Giardia lamblia were freed from cytoskeleton fragments and other cell contaminants by centrifuging in a density gradient. The purified organelles contain many polypeptides, including a set of low-molecular-weight antigens [apparent molecular weights (MWs) = 31, 32, 34, 35 and 37 kD] in the same size range as the approximately 30 kD structural giardins of the cytoskeleton. However, on sodium dodecyl sulphate-polyacrylamide gels, the mobilities of individual flagellar polypeptides do not correspond exactly to the cytoskeleton bands, and, unlike the cytoskeleton proteins, the flagellar components are easily extracted by Triton demembranation. The pattern of flagellar isoforms after isoelectric focussing (IEF) and electrophoresis in two dimensions is also clearly different from that of the cytoskeleton proteins. The fact that at least some approximately 30 kD flagellar antigens are localised by immunofluorescence specifically in the two ventral flagella suggests that these proteins may be components of the paraflagellar structures found beneath the membrane of these organelles. In electron micrographs of the isolated flagella, the paraflagellar rods are seen to bridge the membrane to three adjacent doublet microtubules of the axoneme.