The rapid identification of drug-resistant strains of Mycobacterium tuberculosis is crucial for the timely initiation of appropriate antituberculosis therapy. The performance of the Genotype MTBDRplus assay was compared with that of the Bactec 460 TB system, a "gold standard" culture-based method. The Genotype MTBDRplus assay was quicker and more cost-effective for the detection of rifampin resistance, but it was not as good for the detection of isoniazid-resistant strains in our setting.