Nutrient bioaccessibility and subsequent absorption will be directly influenced by changes in food structure during gastrointestinal processing. The accompanying paper (Tydeman et al. J. Agric. Food Chem. 2010, 58, doi: 10.1021/jf101034a) reported results on the effect of carrot processing on the release of carotene into lipid phases during in vitro gastric and small intestinal digestions. This paper describes results from in vivo digestion of two of the types of processed carrot used previously, raw grated carrot and cooked carrot mashed to a puree. Ileostomy effluents from human volunteers fed meals containing the carrot material were used to study tissue microstructure and carotene release. Raw carrot shreds and intact cells that had survived the pureeing process were identifiable in ileal effluent. The gross tissue structure in the shreds had not changed following digestion. Carotene-containing particles remained encapsulated in intact cells, but were absent from ruptured cells. Microscopy revealed marked changes to the cell walls including swelling and pectin solubilization, which increased in severity with increasing residence time in the upper gut. These observations were entirely consistent with the in vitro observations. It was concluded that a single intact cell wall is sufficient to reduce carotene bioaccessibility from a cell by acting as a physical barrier, which is not broken down during upper gut digestion.