The MHC class II alpha beta heterodimer associates with invariant (I) chain in the endoplasmic reticulum and remains associated until the complex reaches a post-Golgi compartment. During early stages of transport, I chain blocks peptide binding to alpha beta dimers. I chain is proteolytically cleaved in a post-Golgi compartment releasing alpha beta dimers that can bind antigenic peptides and transport them to the cell surface. Human B lymphoblastoid cell lines grown in leupeptin, a sulfhydryl protease inhibitor, accumulate a partial proteolytic product of the I chain called leupeptin-induced protein (LIP). LIP remains associated with alpha beta dimers. We find, using chemical cross-linking, sucrose gradient sedimentation, and size exclusion chromatography, that the alpha beta LIP complex retains the nine-subunit structure described for alpha beta I complexes. Unlike the alpha beta I complex, in certain detergents the alpha beta LIP nonamer is unstable and dissociates into trimers containing one alpha, beta, and LIP molecule. This finding emphasizes the reported stoichiometry of the alpha beta I complex as a nine-subunit structure comprised of three alpha beta I trimers. Also, these data indicate that the region(s) of I chain necessary for retaining the nonameric structure lie within the LIP fragment, but that domains to the C-terminus of the LIP cleavage site act to further stabilize the nine chain structure. In addition, alpha beta I complexes containing forms of human I chain encoding the p35/p43 N-terminal cytoplasmic extension responsible for endoplasmic reticulum retention can transport to post-Golgi proteolytic compartments where LIP is formed.