Anthocyanins are ubiquitous pigments in the human diet, but their metabolic fate is poorly understood. Absorption of these compounds may occur in the stomach, where acidic pH favors anthocyanin stability. The NCI-N87 cell line gastric model was used to examine the effects of anthocyanin chemical structure on their transport and uptake at pH 3, representative of the gastric environment. Chokeberry, containing different cyanidin derivatives, was used to determine the effects of different sugar substitutions; red grape was used as a source of monoglucosylated derivatives of different aglycones. The type of sugar substitution on cyanidin affected both cellular uptake and transport to the basolateral chamber, with cyanidin-3-arabinoside showing the greatest transport and cyanidin-3-glucoside the highest uptake by the cell. The aglycone structure also affected uptake and transport. Anthocyanins bearing B-ring di-substitution, cyanidin-3-glucoside and peonidin-3-glucoside, were transported and taken up the most by cells. Transport through NCI-N87 cells was most efficient for cyanidin-3-glucoside followed by peonidin, delphinidin, pelargonidin, malvidin, and petunidin-3-glucosides, in that order. Cyanidin-3-glucoside was also more efficiently taken up by the cells, followed by peonidin, pelargonidin, delphinidin, petunidin, and malvidin-3-glucosides. Although the metabolism of anthocyanins requires much more study, further evidence of the role of chemical structure is provided.