Gastric cancer (GC) stands as the second most common cause of cancer death for males worldwide, and intestinal metaplasia (IM) is a lesion that precedes GC development. In previous works it was shown that polymorphisms of MUC1 gene are associated with increased risk for GC and IM. The aim of the present study was to evaluate MUC1 gene polymorphism in patients with chronic gastritis from Colombia. A Portuguese population of patients with chronic gastritis was used for comparative purposes. A total of 67 Colombian cases and 52 Portuguese cases were analysed by restriction analysis and Southern blotting. MUC1 allele frequencies were significantly different between the two populations, with an overall prevalence of smaller alleles in Colombian samples. Colombian cases showed a lower prevalence of individuals homozygous for small MUC1 mucins in cases without IM (62.5%) when compared with cases with IM (86.0%). The same trend, although not statistically significant, is observed in the Portuguese population. In conclusion, our study shows that Colombian patients with chronic gastritis have a significantly higher prevalence of small MUC1 alleles than the Portuguese population. Our study also shows that small MUC1 genotypes are associated with increased risk for IM development in Colombian patients.