Proteomics is the term for the large-scale analysis of proteins. Such studies have contributed greatly to our understanding of gene function in the postgenomic era. Besides identification, the characterization of protein function is also a key objective of proteomic research. One of the major challenges for Candida biologists is how to interpret the large amounts of transcriptional analysis data, and assign function(s) to numerous uncharacterized genes, and the proteins they encode. In this regard, the Candida albicans cell wall and its constituents have been a topic of research for many scientists largely due to its importance as a potential target for antifungal therapy and its role in pathogenesis. Thus, the application of proteomic technology to cell wall analysis is timely, and cell wall fractionation followed by identification of cell wall proteins by mass spectrometry is discussed in this chapter.