Metabolic labeling studies suggest that Saccharomyces cerevisiae contains many glycoproteins that are anchored in the lipid bilayer by glycosylphosphatidylinositol membrane anchors. Membrane anchors were purified from a crude yeast membrane protein fraction and analyzed by two-dimensional 1H-1H NMR, fast atom bombardment-mass spectrometry, compositional and methylation linkage analyses, as well as chemical and enzymatic modifications. The yeast glycosylphosphatidylinositol anchors consist of the following structures: ethanolamine-PO4-6(R-2)Man alpha 1-2Man alpha 1-6Man alpha 1-4Glc-NH2 alpha 1-6myo-inositol-1-PO4-lipid, where R is mainly Man alpha 1- (80%) with some Man alpha 1-2Man alpha 1- (15%) and Man alpha 1-3Man alpha 1- (5%). The core region of the yeast anchors (ethanolamine-PO4-6Man alpha 1-2Man alpha 1-6Man alpha 1-4GlcNH2 alpha 1-6myo-inositol-1-PO4) is identical to the conserved core region found in glycosylphosphatidylinositol anchors from protozoa and mammals. The lipid moieties of the total yeast glycosylphosphatidylinositol anchors are mainly ceramides, consisting mostly of C18:0 phytosphingosine and C26:0 fatty acid. However, the lipid moiety of the glycosylphosphatidylinositol anchor of the purified ggp125 protein is a lyso- or diacylglycerol, containing C26:0 fatty acids. This suggests that yeast adds different lipid components to the glycosylphosphatidylinositol anchors of different proteins.