Intestinal absorption rates vary with the nature of the substances involved. In-vitro experiments with cell culture inserts are often conducted to evaluate the intestinal absorption rate. These inserts, however, require large amounts of cells, samples, and culture media, and take a long time to evaluate. To overcome these problems, we developed a microchip-based system that mimics the intestine. The microchip was composed of a glass slide, a permeable membrane, and polydimethylsiloxane (PDMS) sheets, which contained microchannels made by photolithography; Caco-2 cells were cultured on the membrane in the microchip. The system was regulated with a microsyringe pump. We conducted permeation tests; cyclophosphamide, which can permeate the intestinal barrier, displayed a high permeability coefficient and Lucifer yellow, which cannot be absorbed at the intestinal wall, displayed a low permeability coefficient. These results were consistent with those obtained using a conventional method, which supports the validity of our new system. The system realized an 80% reduction of cell consumption.