A repeated or prolonged stimulation with LPS induces in macrophage-lineage cells a refractory state known as endotoxin tolerance (ET). ET curtails inflammation and prevents tissue damage caused by sustained immune activation in sepsis. TNF-α is required for ET induction and it is hypothesized that TNF-α exerts its immuno-modulatory action via ET-associated molecules. In models of TNF-α-driven disease, ET-associated molecules were investigated to determine their role in the progression from acute, self-limiting inflammation to chronic inflammatory disease. An in vitro model of ET was developed to evaluate the gene expression profile of ET macrophages. The ET-associated genes IRAK3, TNFAIP3 and PTPN6 were further investigated in collagen-induced arthritis (CIA). Although arthritic paws had increased macrophage-lineage cell infiltration and high expression of TLRs and TNF-α, the expression of ET-associated genes was not uniformly increased. Tnfaip3 and Ptpn6 were up-regulated in arthritic paws but Irak3, a key molecule in ET which inhibits the MyD88 pathway, was expressed at a lower level than the naà ̄ve control throughout the inflammatory process. CIA was performed in IRAK3^-/- mice and WT controls. In IRAK3^-/- mice the disease was significantly accelerated, inflammatory gene expression was higher in paws, plasma IL1β concentration was higher and there was a decrease in the prevalence of regulatory T cells in spleen and lymph-nodes. We hypothesize that an alteration in IRAK3 gene expression or activity potentiates the development and chronicity of inflammatory disease.