A case-control study for stomach cancer was conducted in a high-risk population in Nariño, Colombia to determine the risk of gastric precancerous lesions associated with salt intake measured by sodium-to-creatinine ratio of a single urine sample. Gastric biopsies and urine samples were collected from 263 individuals. Urinary sodium-to-creatinine ratios were studied in relation to histological data from the biopsies. Significantly high odds ratios for precancerous lesions (chronic atrophic gastritis, intestinal metaplasia, and dysplasia) were associated with higher sodium-to-creatinine ratios. Adjusted odds ratios (OR) of 2.50 for chronic atrophic gastritis and 7.24 for dysplasia were found. The association with intestinal metaplasia was weaker and not significant (OR = 1.57). Furthermore, an excess risk associated with adding salt to food at the table was found among patients with precancerous lesions (OR = 1.80). These findings support the two-step involvement of salt in the process of gastric precancerous lesions.