The Toll-like Receptor 4 (TLR4) is an innate immune protein on cell surfaces that identifies Lipopolysaccharide (LPS) of gram-negative bacteria. Genetic markers associated with innate responses during mastitis could help in selection of cattle to improve disease resistance. The objective of this study was to determine the association between TLR4 gene and clinical mastitis, using selective genotyping method. A total of 270 cows of two extreme groups namely: top clinical mastitis resistant vs. top susceptible ones were selected. For genotyping, the 2 methods of: PCR-RFLP and PCR-SSCP were made use of. Identified polymorphisms induced A-G in exon 2, and C-T in exon 3. Following sequencing, polymorphism effects on clinical mastitis were analyzed using logistic regression. The results indicated that TLR4 gene was significantly associated with clinical mastitis resistance.