SETTING: Although considerable effort has been put into the development and evaluation of new diagnostics for tuberculosis (TB) and multidrug-resistant TB (MDR-TB), little attention has thus far been paid to the technical aspects of initiating quality-assured routine service use. For implementation of the microscopic-observation drug susceptibility (MODS) methodology in the Peruvian reference laboratory network, a laboratory accreditation process was devised; MODS results from an expert reference laboratory (Universidad Peruana Cayetano Heredia [UPCH]) were used as the standard against which implementing laboratory MODS results were judged to ensure that, prior to use for patient care, implementing laboratories achieved the same high performance with MODS as previously demonstrated in the research laboratory. OBJECTIVE: To evaluate the validity of MODS-based accreditation and the concordance of MODS drug susceptibility testing (DST) with molecular testing. DESIGN: Head-to-head comparison of MODS DST results from implementing Peruvian regional reference laboratories and the accrediting expert MODS laboratory (UPCH) with GenoType® MTBDRplus DST. RESULTS: The concordance of phenotypic MODS rifampicin (RMP) DST with GenoType MTBDRplus was respectively 97.4%, 97.9% and 97.1% for the two implementing regional laboratories and UPCH, and respectively 94.7%, 95.7% and 94.6% for isoniazid (INH) DST. CONCLUSION: High and consistent levels of MODS/MTBDRplus concordance for INH and RMP DST confirm the validity of the use of rapid methods as reference standards for accreditation.