In Saccharomyces cerevisiae, glycosylphosphatidylinositol (GPI)-anchored cell wall mannoproteins, including alpha-agglutinin, are secreted to the cell surface through vesicular transport pathways. At the cell surface the GPI anchors are cleaved within the glycan, then transglycosylated to form a covalent cross-link to 1,6-beta-glucan. Among mutants that were temperature-sensitive for growth and for ability to cross-link the mannoprotein alpha-agglutinin to the cell wall, one strain was complemented by BET1, which encodes an ER-Golgi v-SNARE. Temperature-sensitive mutations in BET1 caused aberrations in cell wall structure, including excretion of alpha-agglutinin into the medium, sensitivity to lysis with Zymolyase and hypersensitivity to Calcofluor White. At restrictive temperatures, bet1 mutations block secretion of invertase and other proteins, but alpha-agglutinin was excreted into the extracellular medium. In wild-type parental or bet1 cells, secretion of alpha-agglutinin also continued after protein synthesis was blocked with cycloheximide. This secretion was due to continued export of a significant amount of alpha-agglutinin from compartments distal to the BET1-dependent secretion step. Thus, in bet1 cells the ER-Golgi block allowed secretion to continue, but prevented cell wall incorporation of the alpha-agglutinin. Therefore, a mutation early in the secretion pathway caused aberrant cell wall synthesis by preventing localization of key components required in wall cross-links.