Plasmodium falciparum accumulates the two merozoite surface proteins-1 and -2 during schizogony. Both proteins are proposed to be anchored in membranes by glycosyl-phosphatidylinositol membrane anchors. In this report the identity of these GPI-anchors is confirmed by labelling with tritiated precursors and additionally by specific enzymatic and chemical treatments. Detailed structural analysis of the core-glycans showed that the GPI-anchors of both proteins possess an extra alpha 1-2 linked mannose at the conserved trimannosyl-core-glycan. MSP-1 and MSP-2 labelled with tritiated myristic acid possess primarily radioactive myristic acid at inositol rings in both GPI-anchors. Additionally the hydrophobic fragments released from [3H]myristic acid labelled GPI-anchors were identified as diacyl-glycerols, carrying preferentially [3H]palmitic acid in an ester-linkage.