In federally regulated drug testing, laboratories must identify and quantitate drugs and their breakdown products by gas chromatography-mass spectrometry (GC-MS) to a concentration that is at least 60% below the cutoff concentration for reconfirmation purposes. Use of methamphetamine-d5 as an internal standard in routine testing with derivatization by HFBA was found to contribute m/z 91 and 118 ions to the same ions from the nondeuterated methamphetamine in the specimen. This resulted in poor chromatography and occasionally caused the 91/254 and 118/254 ion mass ratios to exceed the +20% acceptance limit established in the calibration process at low concentrations. The analogues methamphetamine-d8 and -d11 were evaluated for contributions to the nondeuterated methamphetamine ion fragments. Methamphetamine-d8 produced m/z 91 and 118 ions, but in less abundance than methamphetamine-d5. Methamphetamine-d11 was found to produce little or no detectable m/z 91 or 118. Replacing methamphetamine-d5 with methamphetamine-d11 eliminates this problem and allows the assay to consistently produce ion mass ratios and acceptable chromatography sufficient for identifying and quantitating methamphetamine at 60% below the 500-ng/mL cutoff concentration.