Despite current guidelines for tuberculosis (TB) control in health care settings, which focused on smear-positive cases, prevention of nosocomial TB transmission continues to be a challenge. Here, we report the results of the first hospital-wide prospective study applying interferon-gamma release assay to investigate the role of smear-negative, culture-positive index cases in nosocomial TB transmission. We prospectively identified cases of culture-confirmed smear-negative pulmonary TB receiving aerosol-generating procedures (AGPs) and cases of culture-confirmed smear-positive pulmonary TB admitted at a medical center. Nosocomial transmission was evaluated by screening their close contacts for latent TB infection (LTBI) using an interferon-gamma release assay. A total of 93 smear-negative index receiving AGP and 122 smear-positive index were enrolled. Among them, 13 (14.0%) and 43 (35.2%) index cases, respectively, had secondary cases of LTBI (P < .001). Sputum smear negativity (adjusted odds ratio: 0.20 0.08-0.48) and AGP (sputum suction; adjusted odds ratio: 3.48 1.34-9.05) are independent factors of transmission. A similar proportion in the close contacts of the 2 index groups had LTBI (17 15.3% and 63 16.0%, respectively), and the former index group contributed to 21.3% of the nosocomial transmission. Smear-negative, culture-positive index cases receiving AGPs could be as infectious as smear-positive index cases. Hospital TB control policy should also focus on the former group. •The role of smear-negative index cases in nosocomial transmission remains unknown.•Smear-negative cases receiving AGPs could be as infectious as smear-positive cases.•Smear-negative cases may be responsible for 21.3% nosocomial TB transmissions.•Ongoing physician education to optimize the utilization of TB-NAAT is imperative.•Hospital TB control should also focus on smear-negative index receiving AGPs.