Tuberculosis has been given great attention as HIV/AIDS has increased. Because HIV causes a higher tuberculosis risk is becoming more and more important better tuberculosis treatment. This study aimed to compare the smear conversion rate between short course therapy and the tuberculosis treatment with directly observed short course therapy (DOTS), in East Java, Indonesia. The average smear conversion rate in short course therapy among 35,292 cases was 94.40% over 5 year period (1989/90-1993/94). The tuberculosis treatment with DOTS was started in 1994/95. In the first 2 years the smear conversion rate were 97.67% (42/43) and 98.00%(196/200), respectively. The smear conversion rate of the treatment with DOTS was significantly higher compared to a short course therapy (p-value: <0.001). Thus, tuberculosis treatment with DOTS should be promoted. The concept of supervision by health workers or health cadres should be applied considering mostly are given by family members. And there should be readiness of tuberculosis staff to do the treatment with DOTS in all levels to expand the coverage.