Lycopene in fruits and vegetables occurs mostly (80–97 %) in the all-E configuration, whereas a considerable proportion of lycopene in the human body is present as Z-isomers. The Z-isomers offer potentially better health benefits and show improved antioxidant activity in vitro when compared with the all-E-isomer. The absorption of dietary lycopene is a complex process involving transfer of the carotenoid from the food matrix into micelles, uptake by enterocytes, packaging into chylomicrons and finally secretion into plasma. Isomerisation could take place at any of these individual steps. By exploiting in vitro and in vivo models, we traced lycopene isomerisation during absorption using various methods to mimic gastric and duodenal conditions, incorporation into mixed micelles, absorption and metabolism by various Caco-2 cell clones, and performed a postprandial study in human subjects to identify the profile of lycopene isomers in plasma chylomicrons. We demonstrate that all-E-lycopene remains unchanged during its passage in the gastrointestinal tract, including its incorporation into mixed micelles. The key site of lycopene isomerisation is inside the intestinal cells resulting in 29 % of lycopene as Z-isomers. Lycopene isomerisation in the various Caco-2 cell clones is consistent with that observed in human chylomicrons formed in a postprandial state. There is no selection in the release of lycopene isomers from enterocytes. Although there is a huge inter-individual variability of total lycopene absorption reported both in in vitro intestinal cell lines as well as in human chylomicrons, the lycopene isomer profile is quite similar.