Innate immunity is responsible for the initial detection and response to pathogen infection. Because of their role in a host’s defense against viruses, Toll Like Receptors (TLRs) are candidates for studies of resistance or susceptibility to viral infection in cattle. TLR3 is involved in the recognition of viral double-stranded RNA which is known to be generated by most viruses during infection as a replication intermediate for ssRNA viruses. Therefore, in the present study, TLR3 was considered as a candidate molecule for studying certain molecular aspects, since the FMDV RNA undergoes a double stranded “replicative form”. Effort was made to correlate the expression and mutation in terms of SNPs of TLR3. The severity of the disease was graded as ‘more severe’, ‘less severe’ or ‘no disease’. TLR3 was found to increase significantly in case of FMDV infected cattle. Out of the total 40 infected samples subjected for TLR3 expression, 14 samples showed marginal expression of TLR3. Among the others, the fold increase in expression varied from moderate to high level. In ‘less severe’ cases of the disease, TLR3 expression was found to be more and was statistically significant compared to ‘more severe’ group. For studying the polymorphism in the bovine TLR3 gene, two SNPs (rs42852440 and rs42852439) were targeted and both were mostly prevalent in FMDV cases. From the above study it can be concluded that the expression of TLR3 was correlated with the disease in that in the ‘less severe’ cases, TLR3 expression was found to be significantly high compared to ‘more severe’ cases and the presence of SNPs in the coding region was found to exist although there was no statistical correlation with the severity of the disease.