Abstract: Objective To comprehend the situation of external quality assessment (EQA) for M.tuberculosis quality control system in Shanghai, and to evaluate two different quality control modes performed in shanghai. Methods The original mode had been performed from year 2001 to 2003, and the other mode was performed from year 2005 to 2007, were compared for their consistency. Results Using the original mode, the consistent positive rate was 100.0% (2741/2741) and the consistent negative rate was 99.1% (3388/3420) .Using the new mode, the consistent positive rate was 99.5% (656/659) and the consistent negative rate was 99.3% (4575/4605) . Conclusion The difference of the positive and negative rates from the original and new EQA mode is not significant statistically (P>0.05), but the new mode played a greater role in promoting the standardization of sputum smear for microscopic detection.It can effectively reflect the quality of sputum smear, and is convenient for the communication between different laboratories.