By providing innate immune modulatory stimuli, the early life immune system can be enhanced to increase resistance to infections. Activation of innate cell surface receptors called pattern recognition receptors (PRRs) by TLR ligands is one promising approach that can help to control infections as described for listeriosis and cryptosporidiosis. In this study, the effect of TLR2/TLR1 and TLR2/TLR6 agonists was compared when injected into neonatal mice. Surprisingly, the stimulation of TLR2/TLR6 led to the death of the neonatal mice which was not observed in adult mice. The TLR2/TLR6 agonist administration induced higher systemic and intestinal inflammation both in adult and neonatal mice when compared to TLR2/TLR1 agonist. The mortality of neonatal mice was IFN-γ dependent and involved the intestinal production of IL-22 and IL-17A. This study clearly demonstrates that targeting TLRs as new control strategy of neonatal infections has to be used with caution. Depending on its heterodimeric form, the TLR2 stimulation can induce adverse effects more or less severe relying on the age-related immune functions of the host.