The exterior surface of the cell wall of Candida albicans can be hydrophobic or hydrophilic. Hydrophobic cell wall proteins of masses 32-40 kDa from C. albicans demonstrated strong aggregation tendencies which influenced both preparation and analysis. The proteins aggregated at 37°C in water and various buffers. Aggregation of the isolated proteins increased with time, was rapidly promoted by heat (3 min, 100°C), and was influenced by dialysis method, protein concentration, and centrifugal ultrafiltration. The presence of 2% sodium dodecyl sulfate (SDS) and 5% 2-mercaptoethanol (2-ME) inhibited aggregate formation, but heating in SDS and 2-ME did not disrupt pre-formed aggregates. Aggregate sizes in acrylamide gels corresponded to roughly dimer and trimer molecular weights. Electron micrographs of negatively-stained hydrophobic protein samples demonstrated very large aggregates which were not observed in unfractionated cell wall protein samples. The potential impact of hydrophobic protein aggregation upon the ectomural fibrillar structure of the C. albicans cell wall is discussed.