MUC1 is a glycoprotein mucin expressed in apical mammalian epithelial tissues, such as mammalian gland, which the main function is protect the cell surface from the environment microorganisms. Hence, MUC1 gene is a candidate gene to mastitis resistance. The MUC1 molecule is well defined in bovines, which has been associated with a highly polymorphic variable number of tandem repeats region (VNTR), which are highly conserved. However, there is no information about MUC1 for water buffaloes (Bubalis bubalis). Thus, the aim of this study was to identify the VNTR polymorphism of MUC1 gene in water buffaloes of Murrah breed and evaluated the polymorphism associations with economical traits and mastitis resistance. 200 animals from the experimental farm of State University of Sao Paulo (Brazil) were used. Genotyping was performed by the polymerase chain reaction (PCR). The amplified fragments were separated by electrophoresis on 1.5% agarose gel. The length of the alleles was estimated using the GeneRuler plus molecular weight marker. The traits evaluated were: somatic cell count (SCC), fat percentage (%F), age at first calving (AFC), calving interval (CI), fat yield (FY), protein percentage (%P), protein yield (PY) and milk production (MP). The analyses were performed using the PROC MIXED procedure of the SAS program to evaluate the effect of the presence/absence of the MUC1 alleles on each trait. Differences with P < 0.05 were considered significant. Three alleles of different lengths were amplified and named allele 1, 2 and 3. Allele 2 was the predominant with a frequency of 0.56. Genotype 2/3 was the most frequent in all animals with a frequency of 0.41.The statistical analysis considering the presence/absence of the MUC1 alleles revealed that the alleles 1 and 3 were associated with some economic traits. A significant effect for the allele 1 was observed for higher means for SCC (7.52) and %P (4.39). The absence of allele 3 was significantly associated with higher means for PY (82.45) and AFC (862.12). The allele 1 effect for SCC persisted significant after the Bonferroni adjustment. Our data indicate MUC1 gene association with traits related to mastitis resistance like SCC and with economic traits like %P.