This thesis is an investigation of the naturally processed and presented peptides (NPPPs) associated with chicken major histocompatibility complex ('MHC') class II molecules of 'B21' and ' B19' haplotypes. Identification of the NPPPs was to assist determination of putative peptide-binding motifs for the B21 and B19 MHC-II molecules. The B21 and B19 MHC-II molecules were immunoaffinity purified, their associated peptides were acid eluted and sequenced by mass spectrometry (MS). Four and one peptides (of membrane, cytosolic and ribosomal origins) associated with B21 and B19 molecules, respectively, were sequenced. Putative peptide-binding motifs for these molecules were identified and used to scan Marek's disease virus (MDV)-intracellular protein (ICP) 4 and glycoprotein (g) B for peptides that could potentially bind B21 and B19 molecules. For ICP4, 99 and 131, and for gB, 103 and 122 peptides were identified fulfilling the binding criteria for B21 and B19 MHC-II molecules, respectively.