In the preparation of a reference material (RM) for quality assurance, both homogeneity and stability studies are integral parts. In the present study, both homogeneity and stability of a candidate RM for the determination of methamphetamine and amphetamine in hair were examined by an isotope dilution gas chromatography/mass spectrometry (GC/MS) method, which is not only one of the analytical methods validated in our previous study but also one of the primary methods for the preparation of a certified reference material (CRM). Additionally, homogeneity was monitored using a different method: micropulverized extraction followed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), which was fully validated in the previous study. In order to demonstrate the suitability of the method as an isotope dilution with mass spectrometry (IDMS), the extraction efficiency was also determined according to time. Our results showed that the current method, i.e., agitating hair with isotope internal standards in the extraction solvent for 20 h followed by GC-MS, was accepted as an IDMS. No significant difference was observed between bottles of the candidate CRM. The statistical results also showed no significant trends in stability for 92 days at room temperature and 4 degrees C. An inter-laboratory quality assurance program was also performed successfully using this material. The candidate CRM developed in the present study demonstrated its suitability for quality assurance in hair drug analysis. Even though a RM is necessity as a quality control tool, it is not always easy to have an authentic RM containing target drugs and metabolites. Even when an in-house quality control material is used, both homogeneity and stability should be investigated.