An infection with Plasmodium falciparum may lead to severe malaria as a result of excessive binding of infected erythrocytes in the microvasculature. Vascular adhesion is mediated by P. falciparum erythrocyte membrane protein-1 (PfEMP1), which is encoded for by highly polymorphic members of the var-gene family. Here, we profile var gene transcription in fresh P. falciparum trophozoites from Ugandan children with malaria through var-specific DBL1␣-PCR amplification and sequencing. A method for subsectioning region alignments into homology areas (MOTIFF) was developed to examine collected sequences. Specific PfEMP1-DBL1␣ amino acid motifs correlated with rosetting and severe malaria, with motif location corresponding to distinct regions of receptor interaction. The method is potentially applicable to other families of variant proteins and may be useful in identifying sequencephenotype relationships. The results suggest that certain PfEMP1 sequences are predisposed to inducing severe malaria.homology areas ͉ antigenic variation ͉ rosetting P lasmodium falciparum malaria infection is one of the primary contributors to childhood mortality in many developing countries. Despite exhaustive research efforts, no vaccine capable of conferring an adequate level of immunity has been developed to date. Vaccine development is encouraged by the fact that children attain conditional immunity to severe malaria after relatively few infections. However, a lack of insight into the molecular interplay between the parasite and the host continues to thwart efforts at vaccine development. One of the key factors in this process is the ability of the parasite to continually express a plethora of antigenic variants of gene families, whose selection appears to correspond with interactions with the host immune system.Severe malaria, a highly lethal form of the disease, is, in part, attributable to the sequestration of P. falciparum-infected erythrocytes (IE) and uninfected erythrocytes in postcapillary venules of the brain, the lungs, or other organs (1). P. falciparum expresses a number of proteins at the erythrocyte surface that are closely involved in the excessive sequestration characteristic of severe malaria. The polypeptide most closely scrutinized to date, PfEMP1, is a large 200-to 400-kDa clonally variant antigen encoded by a repertoire of Ϸ60 var genes (2). The var genes present a two-exon structure encoding a conserved C terminus that contains a predicted transmembrane region and a polymorphic submodular N terminus. This N terminus region possesses a number of cysteine-rich domains that are intimately involved in the sequestration of the parasite in the microvasculature (3-5). The Duffy binding-like domain-␣ (DBL1␣) located in the Nterminal head structure of PfEMP1 mediates rosetting and endothelial binding of IE. These binding processes occur by means of a range of different receptors, including heparan sulfate, complement receptor 1, and/or the blood group A antigen (6-9). Rosetting and endothelial binding are intimately associa...