Major histocompatibility complex (MHC) class II molecules (MHC II) present exogenous antigens to CD4+ T cells to modulate immune responses. To contact these antigens, MHC II is delivered to the late endosomal MHC class II compartment (MIIC). This compartment has a complex architecture and consists of internal membranes or vesicles surrounded by a limiting membrane. These subdomains have different protein and lipid content. Also MHC II peptide loading is spatially organized in MIIC as it interacts with DM on intralumenal vesicles (ILVs) to bind antigen. How this is controlled is only understood in a sketchy manner. This may involve ubiquitin modification of MHC II, possibly by E3 ligases of the March family. But other proteins are likely involved as well including E3 ligases, deubiquitylating enzymes (DUBs), adaptor, scaffold, motor and vesicular coat proteins. Our lab performed a genome-wide siRNA screen to define novel proteins and pathways involved in MHC II antigen presentation. The data set is used to select candidate proteins involved in targeting MHC II into MIIC. This process involves ubiquitin modifications and various new molecules not considered as yet in this complex pathway. These molecules may be targeted by drugs to manipulate MHC II responses in auto-immunity, transplantation and other disease states.