The co-occurrence of wheat flour fortification with folic acid and iron and gastrointestinal cancer incidences were critically assessed in the East Azerbaijan province in Northwest of Iran. In an ecological design, overall gastrointestinal cancer rate ratios and their 95% confidence intervals (95% CI) were calculated as primary outcome before (2004-2006) and after (2007-2015) the introduction of fortification. No consistent changes were observed in esophageal and gastric cancer, but the rate ratios of colorectal cancer increased significantly after fortification in the 35-54 years age group (women: 2.07, 95% CI: 1.79-2.49; men: 1.59, 95% CI: 1.33-1.89) and the 55-74 years age group (women 1.50, 95% CI: 1.27-1.76; men: 2.51, 95% CI: 2.13-2.95). The increased incidence of colorectal cancer was contemporary with long-term fortification; further investigation is required to establish the associations.