Testing for EBV and KSHV has relied on assays such as immunofluorescence staining and Western blotting of infected cells. Assays using individual viral proteins have also been described. However, in the absence of a global comparison of protein immunogenicity, there has been inadequate information on which to base the choice of antigens to incorporate into these assays. The EBV latency proteins EBNA1, EBNA2, and EBNA3C and the KSHV LANA latency and K8.1 lytic proteins have been widely used as antigens, and these antigens were also frequently detected on the arrays. Our protein array screens also identified the EBV tegument proteins BBRF2, BGLF2, and BNRF1 (FGARAT); the small capsid protein BFRF3; the early protein BRRF1; and the KSHV ORF38 tegument protein as lytic viral proteins that are particularly well recognized by IgG. The screens also identified BBLF4, BCRF1, BKRF3, and BBRF1 as EBV lytic proteins that were well recognized by IgA. It should be noted that the EBV and KSHV proteins for our array were expressed in yeast which do not have the same machinery as mammalian cells for complex glycosylation. It is therefore likely that our assays underestimate the immunological response to glycosylated viral antigens such as the EBV envelope glycoprotein gp350/220 and KSHV K8.1.