Micellar electrokinetic chromatography (MEKC) was successfully coupled to Fourier transform infrared (FTIR) detection, using a micromachined IR-transparent flow cell with an optical path length of 15 mum for the on-line detection of five neutral analytes. Tight connections between the flow cell and the capillaries were achieved by creating a small O-ring of UV-curing epoxy adhesive on the sharply cut capillary ends. The background electrolyte consisted of 15 mM phosphate buffer at pH 7 and 40 mM sodium dodecyl sulfate (SDS). Five analytes (paracetamol, caffeine, p-nitro benzyl alcohol, m-nitrophenol and p-nitrophenol) were successfully separated, yielding detailed IR stack plots that could be used for quantification and identification. Linear calibration graphs were obtained for each individual analyte present in mixtures at concentrations up to 10 mM. The limit of detection (3 S/N) ranged between 1.1 and 1.5 mM (1.2-1.8 ng). Analytes were identified by comparing spectra obtained during the MEKC separation with those resulting from completely filling the capillary with each individual analyte dissolved in the micelle-containing electrolyte. Information on the specific functional groups of all analytes could be elucidated from the spectra. Since FTIR is a nondestructive detection technique, a conventional on-line UV detector was introduced directly after the developed IR flow cell to test the system's performance and to demonstrate that tandem FTIR and UV detection is feasible.