Background: Tuberculosis (TB) is a major public health disease. Early diagnosis and treatment are essential for effective TB control program. In developing countries, diagnosis of TB is mainly by microscopy because of the simplicity of the procedure and cost-effectiveness. In the present study the two methods were compared to derive a conclusion to adopt the better method to provide more effective services for early diagnosis of TB. Methods: This study was conducted to compare the Ziehl-Neelsen (ZN) staining with Fluorescent staining in the diagnosis of primary pulmonary TB patients. A total of 514 pulmonary tuberculosis suspected patients were included for a period of 2 years. Sputum samples were taken and subjected to both ZN staining and fluorescent staining and results were compared. All samples were subjected to solid culture and taking it as gold standard sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of both the staining methods were defined. Results: Out of total 514 samples, 265 (51.56%) were ZN positive and 326 (63.43%) samples were positive for FM. Positive samples detected by ZN staining were compared with positive samples by FM. Sensitivity, specificity, PPV, NPV for ZN microscopy were 80.76%, 97.27%, 98.05% and 74.79% respectively. Sensitivity, specificity, PPV, NPV for FM were 98.71%, 95.63%, 97.47% and 97.76% respectively. Conclusions: In developing country like India where there are large number of cases and gross financial constraints microscopy can be adopted as the main method of diagnosis of pulmonary TB and preferably FM because of higher sensitivity and lesser time taking character of the method.