Others have reported cytokine abnormalities in CSF from subjects with ME/CFS;21 however, this study is the first to employ comprehensive cytokine panels, include both normal control and MS comparator subjects and apply logistic regression and network analysis models. Our results indicate a markedly disturbed immune signature in the CSF of ME/CFS subjects that is consistent with immune activation in the CNS. Persistent secretion of cytokines by activated microglia, brain immune cells of macrophage monocyte lineage, may contribute to this pattern. IL1ra, an endogenous downregulator of IL1 and its inflammatory cascades, has been used to address pathological fatigue in conditions other than ME/CFS, such as histiocytosis.41 Our finding that IL1ra has a negative influence on CSF1, CSF2 and IL17F in ME/CFS, without effects on IL1α or IL1β, suggests a disturbance in IL1 signaling pathways. The role of IL1ra in inhibition of allergic responses42,43 is consistent with reports of an increased prevalence of allergic disorders in some studies of ME/CFS.44,45 IL1ra mediated downregulation of responses to allergic stimuli is associated with lower levels of CSF2 (GMCSF), a key regulator of granulocyte and macrophage maturational pathways.46 The inverse relationship we found between IL1ra and CSF2 in the CSF of cases using a network analysis approach suggests that neuroimmune responses may be shifted toward allergic or Th2 (autoimmune) patterns in the CNS of individuals with ME/CFS. One prior study of CSF cytokines in ME/CFS also found decreased levels of CSF2 (GMCSF),21 a molecule that shifts macrophages toward an M1-like, or inflammatory, phenotype.47 The presence of an allergic-type diathesis in the CNS of individuals with ME/CFS is further supported by the finding of increased CSF levels of CCL11 (eotaxin, a chemokine involved in the selective recruitment of eosinophils, an allergy-associated white blood cell subset48) in ME/CFS subjects relative to ND control subjects. CSF, as a reflection of the microenvironment of the CNS, may provide unique clues to the pathogenesis of ME/CFS. Although increased CSF CCL11 and CXCL10 levels in ME/CFS subjects, along with dysregulation of IL1 signaling, suggest the possibility of an allergic process in central compartments,49,50 such patterns may also be seen in a wide range of CNS infections.51–54 Additional studies focused on delineating the relationships of clinical phenotypes of ME/CFS to immune profiles in both the CSF and the peripheral blood are of paramount importance to investigating potential causes and biomarkers for disease