In order to analyze the clinical impact of immunological alterations in thymectomized children after exposure to a new antigen (tick-borne encephalitis virus (TBEV) vaccine), 17 thymectomized children completed a three-dose immunization regimen. Thymectomized children showed significantly lower TBEV IgG antibody levels after the second vaccination when compared to healthy age-matched controls (n=30) (p=0.03), but a normal response after the third vaccination. Age at thymectomy correlated significantly with the TBEV IgG antibody levels (p=0.04). Thymectomized children also showed significantly lower total counts and percentages for naïve T cells correlating with time after thymectomy (p=0.02), than observed for controls. These changes in T cell subsets and the decreased ability to respond to new antigens in thymectomized children, as observed here, may precede more striking effects such as higher infection rates or autoimmune conditions as they age.