The aim of this study was to investigate the influence of the proteolytic enzyme bromelain on the permeation of heparin across the gastrointestinal epithelial barrier. Stability of the complex and effect of heparin on the enzymatic activity of bromelain was analysed photometrically by measuring bromelain enzymatic activity in complex with the heparin. In vitro permeation studies were performed with Caco-2 cell monolayer and rat small intestinal mucosa in Ussing-type chambers, respectively. Results revealed that enzymatic activity of bromelain remained uninfluenced by the immobilization of heparin on it. Transport studies across Caco-2 cell monolayer and rat small intestine showed that the permeation of heparin could be significantly increased in presence of bromelain. In the study with Caco-2 cells, the most effective molar ratio of bromelain to heparin was 2:1, leading to 6.7-fold improvement in uptake, whereas the molar ratio 1:1 showed the highest permeation enhancing effect in the study on intestinal mucosa. This study provides evidence that heparin and bromelain form stable complexes leading to a significantly improved uptake of heparin.