Toll-like receptors (TLRs) are pattern recognition receptors (PRRs) which detect pathogen-associated molecular patterns (PAMPs) and initiate the innate as well as adaptive immune response. In the present study TLR5 gene from Aseel and White Leghorn was amplified and sequenced by primer walking method. The sequence analysis revealed that Aseel TLR5 shared 97-98% and 98-99% homology with other chicken breeds at nucleotide and amino acid levels, respectively. Further, the TLR5 mRNA expression levels were quantified in different tissues of day-old Aseel and WL chicks by real time PCR assay. TLR5 mRNA expressions were significantly higher in liver, spleen and intestine of Aseel than White Leghorn chicken (P less than 0.01). However, in bone marrow significantly higher expression was observed in WL than Aseel chicken (P less than 0.01) and no significant difference in transcript expression was found in muscle, bursa and heart tissue. In vitro stimulation of PBMCs of Aseel and WL with recombinant flagellin resulted in significantly higher levels of proinflammatory cytokine IL-1â gene expression in Aseel birds than WL. Polymorphisms in ligand binding region, higher transcript expression in tissues at the site of microbial entry and higher pro-inflammatory response to flagellin stimulation in Aseel chicken better immune competence in this native chicken breed.