Expression of immune receptors at the cell surface is a key determinant of immunity. Understanding the molecular mechanisms that govern receptor expression patterns will enable exploitation of receptors in settings of immunotherapy or vaccination. Here, we have aimed to analyse the molecular mechanisms and immune consequences of immune receptor trafficking. One mechanism by which receptor expression is controlled is ubiquitination. Ubiquitination regulates the cell surface display of MHC II (major antigen presenting molecule) and CD86 (co-stimulatory molecule). First, we have identified the ubiquitin codes (ubiquitin chain linkage types) associated with MHC II isolated from primary murine immune cells. Second, we have identified a new role for MHC II ubiquitination in the regulation of dendritic cell homeostasis that involves a surprising intersection between innate and adaptive immunity. Third, we have performed a genome-wide CRISPR/Cas9 screen to identify molecular participants in ubiquitin-mediated immune trafficking. We identified ubiquitin like 3 (Ubl3), a previously uncharacterised mammalian protein, as a novel regulator of MHC II and CD86 trafficking. We describe new roles for Ubl3 in dendritic cells, B cells and thymic epithelium with Ubl3-deficient mice. Finally, we have analysed the trafficking of dendritic cell receptors that are of significant interest for antibody-targeted vaccination, including C-type lectin DEC-205. We have conducted CRISPR/Cas9 screens to identify new genes that regulate both the expression and the internalisation of DEC-205 from the cell surface. In summary, our analysis provides significant advances to understanding how immune receptors are trafficked inside cells with important consequences for immunity.