Mycoplasma hyopneumoniae is the most costly pathogen for swine production. Although several studies have focused on the host-bacterium association, little is known about the changes in gene expression of swine cells upon infection. To improve our understanding of this interaction, we infected swine epithelial nptr cells with M. hyopneumoniae strain J to identify differentially expressed mRNAs and miRNAs. The levels of 1,268 genes and 170 miRNAs were significantly modified postinfection. Up-regulated mRNAs were enriched in genes related to redox homeostasis and antioxidant defense, known to be regulated by the transcription factor NRF2 in related species. Down-regulated mRNAs were enriched in genes associated with cytoskeleton and ciliary functions. Bioinformatic analyses suggested a correlation between changes in miRNA and mRNA levels, since we detected down-regulation of miRNAs predicted to target antioxidant genes and up-regulation of miRNAs targeting ciliary and cytoskeleton genes. Interestingly, most down-regulated miRNAs were detected in exosome-like vesicles suggesting that M. hyopneumoniae infection induced a modification of the composition of NPTr-released vesicles. Taken together, our data indicate that M. hyopneumoniae elicits an antioxidant response induced by NRF2 in infected cells. In addition, we propose that ciliostasis caused by this pathogen is partially explained by the down-regulation of ciliary genes. Respiratory diseases are among the major health problems in the pig farming industry. Mycoplasma hyopneumoniae is the causative agent of swine enzootic pneumonia, a chronic respiratory disease that affects herds worldwide. Although M. hyopneumoniae does not cause high mortality, it is considered the most expensive pathogen for swine production 1. This is mainly due to the costs of treatment and vaccination and to losses related to decreased animal performance. In addition, M. hyopneumoniae is essential for the establishment of secondary pathogens in the host, which leads to a significant increase in mortality 2. M. hyopneumoniae attaches to the cilia of the tracheal epithelial cells with participation of adhesins 3 , resulting in ciliostasis and cell death 4. Besides adhesins, virulence factors are not well understood in this bacterium. Nevertheless, a recent study from our group indicated hydrogen peroxide production from glycerol and myo-inositol metabolism as important traits that might be related with pathogenesis and with the predominance of M. hyopneumoniae in the swine respiratory tract 5 .