This study was conducted to analyze the gene expression of prognostic potential biomarker candidates using the whole blood of cattle naturally infected with Mycobacterium avium subsp. paratuberculosis (MAP). We conducted real-time PCR to evaluate 23 potential biomarker candidates. Experimental animals were divided into four groups based on fecal MAP PCR and serum ELISA. Seven ( KLRB1 , HGF , MPO , LTF , SERPINE1 , S100A8 and S100A9 ) genes were up-regulated in fecal MAP-positive cattle and three ( KLRB1 , MPO and S100A9 ) were up-regulated in MAP-seropositive cattle relative to uninfected cattle. In subclinically infected animals, 17 genes ( TFRC , S100A8 , S100A9 , MPO , GBP6 , LTF , KLRB1 , SERPINE1 , PIGR , IL-10 , CXCR3 , CD14 , MMP9 , ELANE , CHI3L1 , HP and HGF ) were up-regulated compared with the control group. Moreover, six genes ( CXCR3 , HP , HGF , LTF , TFRC and GBP6 ) showed significant differences between experimental groups. Taken together, our data suggest that six genes ( LTF , HGF , HP , CXCR3 , GBP6 and TFRC ) played essential roles in the immune response to MAP during the subclinical stage and therefore might be useful as prognostic biomarkers.