The Class II major histocompatibility molecules are implicated in the initiation of antigen-driven autoimmune responses by CD4-positive T cells. In order to study the structure and function of CD4 and MHC Class II molecules, strategies were developed with the intent of generating secreted forms of these molecules by in vitro mutagenesis of the respective genes. A full length cDNA encoding an expressible human CD4 molecule was mutagenized to introduce a premature stop codon corresponding to residue 367 located 8 amino acids amino terminal to the start of the predicted trans-membrane region. Following DNA-mediated gene transfer of the mutant gene, secreted CD4 was detected in the supernatant of transiently transfected COS-1 cells. Surface expression of the membrane-bound form of CD4 was detected under the same conditions. In an attempt to create a secreted form of the mouse Class II molecule I-Ak the exons encoding the connecting stalk, transmembrane and cytoplasmic domains of both the alpha and beta chains were replaced by the corresponding exons from the gene encoding a secreted Class I-like molecule, Q10b. Transfer of these genes into mouse L cells failed to generate detectable secreted I-A molecules. In view of the secretion of CD4 reported in other mutagenesis studies, it is concluded that very subtle differences in the structure of the COOH-terminus can influence the folding, solubility or transport of the CD4 molecule. In addition, the assembly of heterodimeric Class II molecules may require membrane anchorage of the separate chains or some other contribution from the COOH-terminal domains of the alpha and beta chains.