Microstructures constructed from SU-8 polymer and produced on CaF(2) base plates have been developed for microchip-based analysis systems used to perform FTIR spectroscopic detection using mid-IR synchrotron radiation. The high brilliance of the synchrotron source enables measurements at spot sizes at the diffraction limit of mid-IR radiation. This corresponds to a spatial resolution of a few micrometers (5-20 microm). These small measurement spots are useful for lab-on-a-chip devices, since their sizes are comparable to those of the structures usually used in these devices. Two different types of microchips are introduced here. The first chip was designed for time-resolved FTIR investigations of chemical reactions in solution. The second chip was designed for chip-based electrophoresis with IR detection on-chip. The results obtained prove the operational functionality of these chips, and indicate the potential of these new devices for further applications in (bio)analytical chemistry.