The fuel oxygenate, methyl tert-butyl ether (MTBE), although now widely banned or substituted, remains a persistent groundwater contaminant. Multidimensional compound-specific isotope analysis (CSIA) of carbon and hydrogen is being developed for determining the extent of MTBE loss due to biodegradation and can also potentially distinguish between different biodegradation pathways. Carbon and hydrogen isotopic fractionation factors were determined for MTBE degradation in aerobic and anaerobic laboratory cultures. The carbon isotopic enrichment factor (epsilonC) for aerobic MTBE degradation by a bacterial consortium containing the aerobic MTBE-degrading bacterium, Variovorax paradoxus, was -1.1 +/- 0.2 per thousand and the hydrogen isotope enrichment factor (epsilonH) was -15 +/- 2 per thousand. This corresponds to an approximated lambda value (Lambda = epsilonH/epsilonC) of 14. Carbon isotope enrichment factors for anaerobic MTBE-degrading enrichment cultures were -7.0 +/- 0.2 per thousand and did not vary based on the original inoculum source, redox condition of the enrichment, or supplementation with syringic acid as a co-substrate. The hydrogen enrichment factors of cultures without syringic acid were insignificant, however a strong hydrogen enrichment factor of -41 +/- 3 per thousand was observed for cultures which were fed syringic acid during MTBE degradation. The Lambda = 6 obtained for NYsyr cultures might be diagnostic for the stimulation of anaerobic MTBE degradation by methoxylated compounds by an as yet unknown pathway and mechanism. The stable-isotope enrichment factors determined in this study will enhance the use of CSIA for monitoring anaerobic and aerobic MTBE biodegradation in situ.