Background: Delays in diagnosis and start of effective treatment increase morbidity and mortality from tuberculosis (TB) as well as the risk of transmission in the community; therefore, an operational research directed at increasing our knowledge about the factors affecting these delays has an important role in improving the quality and effectiveness of National TB Programs (NTP). Materials and Methods: This nation-wide cross-sectional study was based on a structured interview with 400 newly diagnosed sputum smear-positive pulmonary TB patients aged over 15, registered at district TB coordination units of the country in a 3-month period in 2003 (from Mid Feb. to Mid May), to determine “the factors affecting the health care system delay". Results: Median Total delay was 92 days (range, 7 - 445). Medians of Patient delay and Health care system delay were 20 (range, 1-381) and 46 (range, 1-444) days respectively; consequently they had a significant difference (p < 0.001). In multivariate analysis, Health care system delay has shown significant increasing association with age (p=0.039), presence of at least a negative sputum smear for Acid Fast Bacilli during the course of disease (p <0.001), attendance in a private clinic as the first health care system (p =0.01), and history of chronic respiratory disease (p =0.044) as well as a decreasing association with the number of symptoms at the first visit (p <0.001) and taking sputum smear or chest X-ray at the first visit (p <0.001). Conclusion: To reduce health care system delay, it is recommended that health care providers especially physicians in private sector be trained and retrained on TB (especially on the mentioned points in the results) at regular intervals. (Tanaffos 2003; 2(8): 55-64)