Infective endocarditis is a disease normally of bacterial cause which affects the endocardic tissue, specifically the valves (native or prosthetic). It is a serious illness and mortality rates remain high, ranging between 20% and 40%. Previous reports have evidenced the potential role of cytokines in the diagnosis of this disease, but no information is available on their relationship with outcome. We recruited 26 consecutive patients with late prosthetic valve endocarditis requiring surgical treatment according to Duke criteria. Eight cytokines were measured in plasma in the first 24 h following diagnosis by using a Bio-Rad multiplex assay. Levels of IL-6, IL-8 and interferon gamma (IFN-γ) were higher in non survivors. Receiver operating characteristic curve analysis evidenced that IL-6, IL-8 and IFN-γ behaved as good diagnostic tests for identifying those patients with fatal outcome (area under the curve, CI 95%, p): IL-6: [0.81 (0.61–1.00) 0.012]; IL-8 [0.76 (0.56–0.96) 0.035]; IFN-γ [0.79 (0.59–0.99) 0.021]. Levels of IL-6, IL-8 and IFN-γ correlated positively between them, indicating that they are produced as consequence of a simultaneous response to the infection. Our findings support the participation of IL-6, IL-8 and IFN-γ in the events linked to fatal outcome in infective prosthetic valve endocarditis.