Epstein-Barr virus (EBV)-specific immunoblot analysis was used to reveal the molecular diversity of immunoglobulin (Ig) G and IgA antibody responses against Epstein-Barr nuclear antigen (EBNA), early antigen (EA), and viral capsid antigen (VCA) in serum samples from patients with nasopharyngeal carcinoma (NPC) and control subjects, by use of immunofluorescence assay (IFA). Control donors (n = 150) showed IgG responses to few EBV proteins—VCA-p18, VCA-p40, EBNA1, and Zebra—and sporadically weak IgA reactivity to EBNA1 and VCA-p18. Patients with NPC stage 1 (n = 6) had similar response patterns. Patients with NPC stage 2–4 (n = 132) showed significantly more diverse IgG and IgA responses to EA and VCA proteins—VCA-p18/-p40, EBNA1, Z-encoded broadly reactive activator, and EAd-p47/54, -DNAse, -thymidine kinase, and -p138. No correlation was found between IFA titers and the number of EBV proteins recognized by IgG or IgA. Our results reveal dissimilarity between EBV polypeptides recognized by IgG and IgA antibodies, which suggests independent B cell triggering events.