IEC6 cells were used as an in vitro model system to study the effects of cell damage caused by mechanical manipulation of intestine epithelial cells. We constructed an apparatus that allowed analyzing the consequences of mechanical compression in a standardized and reproducible manner. Manipulation of IEC6 cells induced necrosis rather than apoptosis, and resulted in release of HMGB1, which is known to function as a trigger of inflammatory responses in vivo. Mechanical damage by traumatic injury of the intestine is accompanied by altered protease activities in the extracellular space, but only little is known about the possible contribution of endo-lysosomal cathepsins. Therefore, we tested the supernatants of manipulated cells in our in vitro model system for proteolytic activity and determined release rates by fluorimetric assays. Endo-lysosomal proteases, such as cathepsins B, D, and L, were released from damaged cells within the first 3 h after manipulation. While cathepsin L re-associated with the surfaces of neighboring cells, cathepsins B and D were present in the extracellular space as soluble enzymes. We conclude that our apparatus for mechanical manipulation can be used to approach surgical trauma, thereby focusing on epithelial cells of the intestine mucosa.