Introduction: Innate immunity significantly participates in the tissue repair process. It has been documented that breastfeeding may alter immune responses. Thus, this project was designed to evaluate the effects of breastfeeding on the levels of TLR1-4, TNF-α, TGF-β, CCL2, and CCL3 in the prepuce tissue of neonates.Material and methods: This project was performed on the 90 samples (45 cases with breastfeeding and 45 cases without breastfeeding) of prepuce tissue of neonates. The tissues were homogenized and mRNA levels of TLR1-4 and protein levels of TNF-α, TGF-β, CCL2, and CCL3 were evaluated by Real-Time PCR and ELISA techniques, respectively.Results: Protein levels of TNF-α, CCL2, and CCL3 and mRNA levels of TLR4 were significantly decreased in the cases without breastfeeding when compared to the neonates with breastfeeding. There was a significant negative correlation between duration of pregnancy and mRNA levels of TLR1 in the neonates without breastfeeding.Conclusion: Due to the results, breastfeeding can modulate the expression of TLR4 and its related cytokines/chemokines to improve its wound healing and fight against pathogens.