We performed a prospective study to evaluate the abilities of inflammatory cytokines to rule out the potential risk of sepsis and intracranial infection and to estimate the function of inflammatory cytokines in discriminating Gram-negative bacteria from Gram-positive ones through ROC analysis. During the course of the study, Levels of serum inflammatory cytokines were measured by flow cytometry at the onset of diseases of patients who suffered from sepsis or intracranial infection. A total of 299 cases of sepsis and 43 cases of intracranial infection were observed during the study. It is noticed that there is no difference of inflammatory cytokine levels between sepsis group and intracranial infection group. The area under ROC curve (AUC) of cytokines, such as IL-2, IL-6 and IL-10 were 0.901, 0.86, 0.888, respectively, which was employed to rule out the diseases of sepsis and intracranial infection. Through comparisons with the patients who were infected by Gram-positive bacteria or Gram-negative ones, it is estimated that IL-6 and IL-10 sharply elevated in patients with Gram-negative bacteria infection (median levels, pg/mL: IL-6: 116.6 vs. 25.4, P = 0.000; IL-10: 13.7 vs. 6.3, P = 0.000). Additionally, IL-2 significantly decreased when patients suffered from Gram-negative bacteria infection (median levels, pg/mL: IL-2: 2.2 vs. 2.7, P = 0.031). The AUCs for detecting cytokines, including IL-2, IL-10 and LOGREGR.Pred_IL-2+IL-10 were 0.581 (95% CI, 0.526 to 0.634), 0.661 (95% CI, 0.608 to 0.712) and 0.735 (95% CI, 0.685 to 0.782), respectively, which was used to evaluate the function of inflammatory cytokines in discriminating Gram-negative bacteria from Gram-positive ones infection. This paper indicates that IL-2, IL-6 and IL-10 are effective biomarkers to rule out sepsis and intracranial infection. Additionally, the combination of IL-2 and IL-10 is an effective biomarkers to diagnose whether patients afflicted by Gram-negative bacteria.