The enteropathogen Salmonella Typhimurium is one of the main causes of porcine and human enterocolitis. We have used a 2-DE, MALDI-TOF/TOF-based approach to characterize in vivo proteome changes in porcine ileum mucosa after pathogen interaction. Ileum samples from non-infected and orally infected animals were collected at 2 days post infection and S. Typhimurium presence was confirmed by immunohistochemistry. Fifty one proteins, involved in immune response (acute phase response, inflammation and immune response regulation), apoptosis and pathogen-mediated cell invasion, were identified as being differentially expressed after pathogen challenge. Overall, anti-inflammatory signals and a possible down-regulation of dendritic cell maturation were observed. According to this, we identified the up-regulation of FK506-binding protein 4 (FKBP4), a negative regulator of the transcription factor IRF4 (interferon regulatory factor 4), implicated in Th2 and Th17 response. Transcriptional analysis using RT-qPCR indicated a general trend toward down-regulation of Th2 and Th17 cytokines genes, which would be in agreement with an IRF4 reduced transactivation activity. On the other hand, proteins that could be involved in maturation of Salmonella-containing vacuole and intracellular pathogen survival were up-regulated. Results derived from this study would be valuable to better characterize a possible pathogen led modulation of host responses in vivo.