OBJECTIVE To provide theoretical evidence for studying the molecular pathogenesis of human cerebral malaria. METHODS The expressions of Plasmodium falciparum erythrocyte membrane protein 1(PfEMP1) on the surface of parasitized erythrocyte (PE) specimens from 19 cases of cerebral malaria patients in Yunnan Province were quantitatively analyzed by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) technique. 43 patients of falciparum malaria, 9 patients of vivax malaria and 6 healthy controls were also investigated. RESULTS The expressions of higher molecular mass (Mr) 260-320 kDa forms of PfEMP1 were found on PE from cerebral malaria patients. By contrast, the expression of PfEMP1 and P. vivax erythrocyte membrane protein (PvEMP1) on PE from falciparum malaria patients and vivax malaria patients had a PfEMP1 with Mr 240 kDa and a PvEMP1 with Mr 180 kDa band, respectively. Healthy controls expressed an EMP of Mr 140 kDa. CONCLUSIONS The binding of 260-320 kDa PfEMP1 proteins expressed on PE from cerebral malaria patients to diverse receptor molecules on the endothelial cell(EC) of the cerebral microvessels such as CD36, thrombospondin (TSP), intercellular adhesion molecule 1(ICAM-1), vascular cell adhesion molecule 1(VCAM-1), endothelial leukocyte adhesion molecule 1(ELAM-1) and chondroitin sulfate A (CSA) might be the molecular basis for the pathogenesis of cerebral malaria.