Cell culture models are useful tools to study the uptake of drugs across the barriers of the human body, like the intestine, the skin or the blood-brain barrier. Cell-based in vitro models not only help to reduce the number of animals used but are also much faster to perform, more cost effective and give more reproducible data than animal studies. Given the increasing number of new drugs and chemicals under development, there is an urgent need for the establishment of such in vitro models. However, the validity of such in vitro models is reflected by its ability to accurately predict the behaviour of a substance at the corresponding in vivo barrier. Here, we compare a well-established cell culture model for the intestine, based on Caco-2 colon carcinoma cells, with a primary cell culture model of the blood-brain barrier. We find that Caco-2 cells and cells of the blood-brain barrier have different barrier properties. Therefore, cells used for cell-based assays should be derived from the corresponding tissue to reflect the in vivo barrier characteristics.