Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a common contaminant at explosives production sites. Here, we report on the use of compound-specific isotope analysis of RDX to obtain ?15N and ?18O enrichment factors during biodegradation in batch cultures. A new preparation method has been developed based on RDX purification using thin-layer chromatography. RDX is then subjected to an elemental analyzer coupled with an isotope-ratio mass spectrometer (EA-IRMS). The precision of the method shows standard deviations of 0.13‰ and 1.18‰ for ?15N and ?18O, respectively, whereas the accuracy of the method has been checked routinely, adhering to external standards. The method was applied to RDX samples subjected to biodegradation under aerobic or anaerobic conditions. Enrichment factors under aerobic conditions were -2.1‰ and -1.7‰ for ?15N and ?18O, respectively, and under anaerobic conditions, -5.0‰ and -5.3‰ for ?15N and ?18O, respectively. The results of this study provide a tool for monitoring natural attenuation of RDX in a contaminated environment.