The present study describes the application of sodium dodecyl sulfate micellar electrokinetic chromatography (SDS MEKC) for the fast analysis of TNT biotransformation products in the aqueous phase of anaerobic sludge cultures. SDS MEKC was performed using a Hewlett-Packard HP 3D CE capillary electrophoresis system with photodiode array detection. In a single sample injection the SDS MEKC method detected 2,4,6-trinitrotoluene (TNT), 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT), 4-hydroxylamino-2,6-dinitrotoluene (4-HADNT), 2-amino-4,6-dinitrotoluene (2-ADNT), 4-amino-2,6-dinitrotoluene (4-ADNT), 2,4-diaminonitrotoluene (2,4-DANT), 2,6-diaminonitrotoluene (2,6-DANT), and 2,4,6-triaminotoluene (TAT). Analyte peaks were verified using visible/ultraviolet photodiode array spectra from commercial standards and periodic analyses using electrospray ionization liquid chromatography mass spectrometry (ES-LC-MS). A time course study constructed from the SDS MEKC data provided supporting evidence for the stepwise reduction of TNT to TAT. The SDS MEKC method was judged to be of practical value for the identification of polar and moderately polar TNT biotransformants in place of HPLC and LC-MS methods, with significant reduction in material expense and analysis time.