We sought to determine whether patients who had therapy failure with increasingly drug-resistant strains of tuberculosis had primary or acquired drug resistance, by genotyping the initial and subsequent drug-resistant clinical isolates of Mycobacterium tuberculosis collected from patients by the Shanghai Centers for Disease Control and Prevention over the course of a 5-year period. The vast majority of patients (27/32) had primary drug resistance, indicating transmission of a drug-resistant strain of M. tuberculosis. Only 16% (5/32) had acquired drug resistance because of a poor treatment regimen or nonadherence to an adequate regimen. Our findings highlight the urgency of increasing efforts to interrupt the transmission of drug-resistant tuberculosis in communities and facilities in Shanghai, China.