To detect the linkage between single markers of microsatellite type and mastitis incidence in Egyptian buffalo three markers (BM1258, BM1443 and BM1818) and one hundred twenty-three lactating animals were used. The selected animals were tested using Modified White Side Test (MWT) to screen animals for mastitis. Non-denatured polyacrylamide gel was used to determine the sizes of the PCR amplified products using reference animal to verify the allelic sizes obtained. For each marker, the frequencies of alleles and genotypes for both positive and negative animal groups were compared by using the chi-square test and the Fisher's exact test. The odds ratios calculated as an estimate of relative risk of mastitis incidence associated with each microsatellite genotypes. A positive mastitis test reaction (MWT) was revealed in 19.5% of total samples. For BM1258, BM1443, and BM1818, the number of alleles was found to be 4, 3 and 5, respectively. The polymorphism in all three studied loci was high (PIC>0.5). The genetic parameters of these loci, including observed and expected heterozygosity, were estimated using full characterizations of this set of three polymorphic loci. The polymorphic information content, heterozygosity, and number of successful alleles of the studied loci showed that BM1443 had the lowest variability and BM1818 had the highest variability, with 0.597 and 0.757, respectively. The overall effects of the three studied markers on mastitis incidence were significantly (P<0.05) different. The genotypes combination ‘72/79', ‘74/74', and ‘79/82' at BM1258 loci; ‘78/78' and ‘88/88' at BM1443 loci, were observed only in the mastitis free animals. On the other hand, BM4505 loci genotypes were found in the positive populations except the combination of genotypes 134/134, 134/140 and 134/144 animals. The information observed in the present study, could be valuable for improving mastitis resistance in Egyptian buffalo breeds through using molecular tools