Early nutritional aggressions promote epigenetic adjustments that culminate in the loss of phenotype plasticity (with permanent long-term modifications). Maternal diet and inadequate neonatal nutrition can result in fetal programming that presents susceptibility to infections in adult life. Thus, it becomes essential to verify the impacts of neonatal malnutrition (even following nutritional replacement) on the immunological response to methicillin resistant Staphylococcus aureus (MRSA) infections. Male rats were divided into two distinct groups: Nourished and Malnourished. After isolation of mononuclear cells, four systems were established: negative control, positive control and two testing systems, (MSSA and MRSA). Tests were performed to analyze expression of TLR-9, NF-kB, IL-1β, IL-18 and IL-33. For statistical analysis, we used the Student t and ANOVA tests p < 0.05. Even after nutritional replacement, malnutrition in the neonatal period compromised the animals' weight gains p < 0.05. There was a reduction in the expression of the immunological response in the positive control, however deregulation was observed in the gene expression of MRSA-infected macrophages, with a reduction in TLR-9 expression, and overexpression in NF-kB and cytokines p < 0.05. Puppies inflicted with protein-calorie malnutrition were compromised; (long-term) body growth and immune response. In the infectious scenario, immune collapse is reflected in inflammatory response exacerbation with a likely histolytic character. Immune disabling (resulting from gene expression deregulation) causes susceptibility to infections due to ineffective recognition, intense pro-inflammatory mediation, and cell death. It is suggested that neonatal malnutrition can program susceptibility to multiresistant bacterial infections, and generally favors a triggering of more intense confrontations with fatal outcomes.