Recently the primary structure of the structural proteins of the flaviviruses West Nile (WN) virus (Castle et al., 1985; Wengler et al., 1985) and yellow fever (YF) virus (Rice et al., 1985) have been determined. As a first step in a further characterization of the organization of the structural proteins we have now studied the disulfide bridges present in the WN virus membrane proteins. All three membrane proteins, pre M, M, and E, were analyzed. The results obtained can be summarized as follows: The pre M proteins of both WN and YF virus each contain 6 cysteine residues and the position of all of these residues is strictly conserved between both viruses. The M proteins of both viruses do not contain cysteine residues. The E proteins of these viruses contain 12 cysteines and the position of all of these residues is strictly conserved between both viruses. All cysteine residues of the WN virus-derived membrane proteins are present as intramolecular disulfides. The six disulfide bridges generated from the 12 cysteine residues in the WN virus-derived E protein have been identified as follows: Cys 1-Cys 2; Cys 3-Cys 8; Cys 4-Cys 6; Cys 5-Cys 7; Cys 9-Cys 10; Cys 11-Cys 12. The analyses of the amino acid sequence conservation between the E proteins of YF and WN virus and the characterization of the disulfides have been used to develop a description of the E protein in which the molecule is assumed to be composed of the segments R1, L1, R2, L2, and R3 followed by a membrane anchor region at the carboxy-terminal region of the molecule. Computer analyses of the hydrophilicity and of the secondary structure indicate that the R1 region might contain a cluster of viral epitopes.