Erythrocyte membrane-associated antigens of Plasmodium falciparum have been of long-standing interest as potential adherence receptors and vaccine candidates. We recently identified in trophozoite-stage infected erythrocytes a novel high molecular weight erythrocyte membrane-associated protein of P. falciparum, PfEMP3, defined by Western blotting with the rat monoclonal antibody 12C11. Genomic clone λ12.1.3 and cDNA clone p12.2 contain nucleic acid sequences encoding PfEMP3. Analysis of Malayan Camp strain parasites by sodium dodecyl sulfate-polyacrylamide gel electrophoresis on 5% gels revealed that PfEMP3, defined by Western blot, has the same relative molecular weight (Mr) as the surface-exposed protein PfEMP1 defined by cell surface iodination. We show here that PfEMP3 is distinct from PfEMP1 by three criteria. First, 125I-labeled PfEMP1 was resolved from PfEMP3 by extended migration on 4% gels. Second, in two strains of P. falciparum in which 125I-PfEMP1 has a different Mr, PfEMP3 had the same Mr. Third, immunization studies were performed with fusion proteins derived from clones λ12.1.3 and p12.2. Although one rabbit, Rb 05.75, immunized with the PfEMP3-derived fusion protein βgal12.1.3, produced a serum that strongly immunoprecipitated PfEMP1 as well as PfEMP3, most sera immunoprecipitated only PfEMP3. Furthermore, immunoprecipitation of PfEMP3 by Rb 05.75 serum was blocked by the glutathione S-transferase 12.1.3 fusion protein, whereas immunoprecipitation of PfEMP1 was unaffected. Therefore, we conclude that PfEMP1 and PfEMP3 are antigenically distinct.