Dissecting variation in gene expression between infected and healthy controls for the genes involved in pathways of immune response to Mycobacterium avium subsp. Paratuberculosis (MAP) infection will allow us to test the hypothesis that variation in expression of these genes influences the disease status in animals. Thus the objective of this study was to analyze differential expression profiles of TLR2, TLR4, IFN-ã, IL2, IL8, IL16 and TNF genes using qRT-PCR in Mycobacterium avium subsp. Paratuberculosis infected cattle vis a vis healthy controls and to assess whether any inherent gene expression patterns are visible for these key innate immune response genes. In the present investigation, distinctive gene expression patterns between PBMCs of healthy cattle and those exposed to MAP. Highest fold change expression was found in IFN-ã gene which was significantly upregulated (7.24 fold, p = 0.0367) in PBMC’s of MAP infected cattle vis a vis healthy controls Expression of TLR2 and IL8 genes were also significantly upregulated in PBMC’s of MAP infected cattle as compared to healthy cattle. Whereas TNF and IL2 genes revealed significant repression in mRNA expression in PBMC’s of MAP infected cattle relative to healthy controls. However in case of TLR4 and IL16 genes, non significant differences were observed for mRNA expression between PBMC’s of MAP infected cattle and Healthy controls. Our results indicate that differences at mRNA level can be utilized in biomarker based segregation of infected and healthy and understanding host-pathogen interactions.