Lysosomal proteinases are involved in two critical stages of MHC class II-mediated antigen presentation, i.e., degradation of invariant chain, a chaperone molecule critical for MHC class II assembly and transport, and generation of class II-binding peptides in the endocytic compartment. We found that two lysosomal cysteine proteinases, cathepsins S and L, were found to be differentially expressed in different types of "professional" and "nonprofessional" antigen presenting cells, including B cells, macrophages, specialized thymic epithelium, intestinal epithelium, and dendritic cells. In this chapter, our recent studies on the role of cathepsin S and L in MHC class II-mediated antigen processing and presentation in these cells types are highlighted.