Peptide-class II complexes are assembled in endocytic, lysosome-like compartments where newly synthesized class II molecules are targeted from the trans-Golgi network (TGN). Recent studies have implicated phosphatidylinositol 3-kinase (PI3-kinase) as an essential component in membrane trafficking from the TGN to lysosomes. Here, using subcellular fractionation, we show PI3-kinase activity associated with subcellular fractions which contain the class II peptide-loading compartment (IIPLC) in B cells. At concentrations required for inhibition of PI3-kinase activity in vivo, wortmannin blocked the processing and presentation of antigen by B cells to T cells. Treatment of B cells with wortmannin significantly limited the proteolytic degradation of invariant chain and the formation of peptide-class II complexes. Subcellular fractionation coupled with pulse-chase analyses showed that invariant chain and class II molecules trafficked to the IIPLC in wortmannin-treated cells. However, wortmannin prevented the maturation and correct targeting to the IIPLC of cathepsin D, a protease necessary for the degradation of invariant chain and assembly of processed antigen-class II complexes. These results suggest that li-class II complexes traffic to the IIPLC via a pathway that is relatively insensitive to wortmannin, but suggest a role for PI3-kinases in the trafficking of other components necessary for the assembly of processed antigen class II complexes to the IIPLC.