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Mucosal antibody response in lower respiratory tract to COVID-19 vaccines is less studied. This cross-sectional study evaluated the respiratory mucosal antibody response in subjects vaccinated with Aikewei or CoronaVac inactivated COVID-19 vaccines. A total of 39 participants were enrolled June 7 to September 15, 2021, including 16 patients who underwent pneumonectomy and 23 patients who underwent bronchoscopy. IgG to nucleocapsid (N) and spike (S) protein of SARS-CoV-2 (anti-N/S IgG), receptor-binding domain (RBD) of S (anti-RBD IgG), and IgA to N (anti-N IgA) were measured with chemo-luminescence immunoassays. Three patients without vaccination and 10 patients vaccinated with one dose showed negative for these antibodies in peripheral or alveolar blood samples or bronchoalveolar lavage fluid (BALF). Of the 12 patients with pneumonectomy vaccinated with two doses, 11 (91.7%), and 10 (83.3%), and 1 (8.3%) were positive for anti-N/S IgG, anti-RBD IgG, and anti-N IgA in peripheral blood, respectively, whereas the positive rates in alveolar blood samples were 66.7% (8), 66.7% (8), and 0%, respectively, and the median level of anti-N/S and anti-RBD in alveolar blood samples was each significantly lower than that in peripheral blood (10.16 vs. 22.18 AU/ml; 10.24 vs. 15.47 AU/ml, both p = .001). Among patients with bronchoscopy, 92.9% (13) of 14 subjects vaccinated with two or three doses showed positive for both anti-N/S IgG and anti-RBD IgG and 7.1% (1) was anti-N IgA positive in peripheral blood; however, all these 14 subjects showed negative in BALF. Together, the results indicate that inactivated COVID-19 vaccines rarely induce mucosal antibody response in the lower respiratory tract.