Background Illness-related costs experienced by tuberculosis patients produce a severe economic impact on households, especially poor families. Few studies have investigated the full costs, including direct and indirect costs, at the patient and household levels in southeast China. Methods A case follow-up study was conducted in the Bao'an district of Shenzhen City, China. Eligible new and previously treated individuals with pulmonary tuberculosis (TB) during January 1 st 2013 to June 30 th 2013 were enrolled. Medical and non-medical costs as well as income loss were calculated in diagnosis and treatment periods, respectively. Factors associated with costs due to TB diagnosis, treatment and TB care (diagnosis + treatment) were explored respectively with a linear regression model. Results Of the total 514 TB patients enrolled, 95% were from the migrant population, and 65% were males, with a mean age of 32.25 (±10.11). The median costs due to TB diagnosis and TB treatment were 79 United States dollar (USD), 748USD (6.2897 China Yuan (CNY) = 1USD, 2013) per patient, respectively. The median costs due to TB care (diagnosis and treatment) per patient was 1218USD, corresponding to 26% of patients' annual income preillness. Those who visited more times to health facilities, hospitalized, received higher education, or occupied in national civil servant/services/retired staff might expense more before diagnosis. Costs due to TB treatment was significantly higher among migrant patients, sputum smear positive patients, and widowed/divorced population. Factors associated with less total costs were native patients, fewer times of visiting to health-care facilities and those with no hospitalization history due to TB.