Chronic multi-symptom illness (CMI) is a broad term utilized by the Department of Veterans Affairs to refer to complex conditions of unknown etiology where individuals experience symptoms that lack a clear medical diagnosis. In this study, we sought to determine if herpesvirus reactivation and the antiviral response could be involved in CMI. Longitudinal serology studies conducted in two military veteran cohorts diagnosed with CMI or Gulf War Illness (GWI) revealed an increased prevalence of IgG (55% and 83%, respectively) and IgM antibodies (80%-90% and 100%, respectively) to the deoxyuridine triphosphate nucleotidohydrolase (dUTPase) protein of multiple herpesviruses compared to age/gender-matched healthy controls (5% and 7% for IgG and IgM respectively, p < 0.001) by ELISA. Despite the ongoing viral reactivation in CMI veterans, IFN-γ levels surprisingly stayed mostly unchanged from healthy control levels, while in GWI were significantly upregulated. Interestingly, MCP-1/CCL-2 levels were significantly increased in some CMI veterans compared to GWI and healthy controls (p = 0.0009). Our data provide evidence suggesting aberrant antiviral response and immune dysfunction in CMI veterans and supports the premise that decreased serum levels of IFN-γ together with heightened MCP-1 and dUTPase antibodies to multiple herpesviruses may be useful to identify CMI veterans with deficient antiviral response.