Abstract Background Taiwan has integrated the previous vertical tuberculosis (TB) control system into the general health care system. With the phase out of the specialized TB care system and the declining TB incidence, it is likely that clinical workers become less familiar with the presentation of TB, resulting in delay in TB diagnosis and treatment. Methods We used the detailed information of health care visits in the Taiwan National Health Insurance database to analyze the temporal pattern of the health system delay (HSD) among 3,117 patients with TB between 2003 and 2010. Results The median HSD was 29 days (interquartile range 5–73 days), and the median delay increased from 26 days in 2003 to 33.5 days in 2008, thereafter slightly decreased to 32 days in 2010. Patient factors associated with a longer HSD included: aged 45–64 and ≧65 years (as compared to aged