Microfluidics is a technology that had emerged over the past decade and it has a great potential for cell biology research. The opportunity of creating and manipulating micrometer sized channels and other geometrical structures offers new opportunities of designing and performing cell biological experiments while reducing time and costs. S-layer proteins are self-assembling proteins which have shown a great potential for revolutionizing specific immunotherapy (SIT). The two S-layer proteins rSbsC31-920 and rSbpA31-1068 and their fusion products with the major birch pollen allergen Bet v1 were investigated for their cytotoxicity on human cell lines (HUVEC, HepG2 and NHDF) within static and µ-fluidic systems. The advantage of using µ-fluidic systems for the analysis of cytotoxic effects is not only a reduced material consumption but also the mimicking of forces naturally acting on cells within the vascular system as it also allows the demonstration of different material-cell interactions than those achievable within conventional cell culture systems.