Oxidative stress, one among the several factors responsible for the gluten toxicity in celiac disease, together with inflammation and duodenal mucosal injury, are only partially reduced by the gluten-free diet. Thanks to their phenolic profile, the pigmented varieties of corn could be an interesting source of dietary antioxidants for the formulation of new gluten-free ingredients. The aim of this research was: (1) to characterize the phenolic profile and the associated antioxidant properties of corn samples with different pigmentation, using spectrophotometric and chromatographic techniques and (2) to assess the stability of anthocyanins during the gastro-intestinal digestion. The pigmented varieties showed a significantly higher content of polyphenols compared to the common yellow varieties and, as a consequence, a higher antioxidant activity. Although corn is among the cereals most frequently used in gluten-free products, it can produce an inflammatory response in some celiac patients. Therefore, after the chemical characterization, the safety of the pigmented varieties for celiac patients was confirmed using different in vitro models (cell agglutination test and the measure of transepithelial electrical resistance). Although in vivo studies are necessary, the data collected in this study underline that the pigmented corn could have a role in reducing the oxidative stress at the intestinal level in celiac subjects.