We investigated the predicted function of proteins eluded from human MHC class Ⅱ molecules.Peptides that arepresented by MHC class Ⅱ were obtained from the SYFPEITHI database and the corresponding proteins werefound in the SWISSPROT database.The functions of these proteins were predicted using the protfun server.Ouranalysis showed that human proteins presented by MHC class Ⅱ molecules are likely to be in the cell envelope,be areceptor or involved in immune responses.Presented proteins from bacteria and virus,on the other hand,are morelikely to be involved in regulatory functions,translation,transcription as well as replication.These results can leadto better understanding the autoimmunity and the response to infections.Cellular & Molecular Immunology.2005;2(1):49-56. We investigated the predicted function of proteins eluded from human MHC class II molecules. Peptides that are presented by MHC class II were obtained from the SYFPEITHI database and the corresponding proteins were found in the SWISSPROT database. These functions of these proteins were predicted using the protfun server. Ouranalysis showed that human proteins presented by MHC class II molecules are likely to be in the cell envelope, be areceptor or involved in immune responses. Presented proteins from bacteria and virus, on the other hand, are more likely to be involved in regulatory functions, translation , transcription as well as replication. these results can lead to better understanding the autoimmunity and the response to infections. Cellular & Molecular Immunology. 2005; 2 (1): 49-56.