Mucins exhibit a high degree of genetic polymorphism because of the presence of a variable number of tandem repeats. The aims of this work were to describe the MUC6 gene polymorphism in the Portuguese population and to evaluate whether MUC6 gene polymorphism was involved in individual susceptibility to gastric cancer development, as observed previously for the MUC1 gene. We found that the 10 alleles identified in the population of blood donors (n = 376), by Southern blot analysis, were also found in gastric cancer patients (n = 157). However, significant differences in allelic frequencies between the two populations were observed for 4 of the 10 alleles, in agreement with those described previously for the MUC1 gene; the largest allele was more frequent in blood donors, and smaller alleles were more frequent in gastric cancer patients. Our results suggest that MUC6 gene polymorphism is involved in the predisposition to gastric carcinoma development.