Therapeutic responses to interferon-a (IFN-a) therapy in patients with malignancies are at least in part from the effects of IFN-a on the enhancement of anti-tumor immune responses. Antigens responsible for immune responses enhanced by IFN-a remain largely unknown. Polycythemia vera (PV) is a myeloproliferative disease (MPD) resulting from the clonal expansion of a pluripotential hematopoietic precursor cell. IFN-a therapy induces a complete remission in ~50% of PV patients, thus making PV a good model to study the molecular mechanism of the cytokine-enhanced immune responses against tumors. We hypothesized that IFN-a enhances anti-PV immune responses by modulating the expression of non-mutated self-antigens. We identified three novel MPD antigens by applying a technique, termed serological identification of tumor antigens by expression cDNA cloning (SEREX), to screen a human testis cDNA library with sera from three PV patients who responded to IFN-a therapy. Of these three novel SEREX antigens, MPD5 belongs to the newly identified group of unconventional cryptic antigens. These unconventional antigens are encoded by either the introns of genes, or the untranslated regions of mRNAs. MPD5 is the antigen encoded by the complementary strand of the intron 1 region of NEK-6 gene. Two additional MPD antigens, MPD13 and MPD67, are conventional antigens, which are encoded by the genes with conventional exon/intron structures. Our results showed that these novel MPD antigens elicit potent IgG antibody immune responses in the sera of patients with PV, as well as patients with chronic myelogenous leukemia who responded to IFN-a treatment and in patients with prostate cancer, suggesting that these antigens are broadly immunogenic. Previous reports showed that unconventional antigens can elicit cellular T cell mediated responses. Our data demonstrated that these antigens also elicit humoral IgG antibody responses, which can be further enhanced by IFN-a therapy. These findings provide new insights into the molecular mechanism underlying the regulation of the self-antigen repertoire including both conventional antigens and unconventional antigens, in eliciting anti-tumor immune responses in responses to IFN-a therapy, and suggest their therapeutic potential as the targets of novel immunotherapy for MPD.