AbstractThe invariant chain (Ii) is a chaperone that regulates assembly and transport of class II MHC molecules. In the absence of the lysosomal protease cathepsin S (CatS), degradation of Ii is impaired and an Ii remnant that extends from the N terminus to about residue 110 accumulates in class II MHC‐positive endosomal compartments, which are enlarged in size and lack multivesicular morphology. In primary B cells examined in vitro and in lymph nodes examined by immuno‐electron microscopy, CatS controls architecture of class II‐positive endosomal compartments. In a compound mutant mouse that lacks both CatS and Ii, the normal size of endosomes in class II‐positive cells is restored, although internal endosomal membranes are absent. Proper degradation of Ii is thus essential for normal endosomal morphology in antigen‐presenting cells in vivo.