Heparin-binding hemagglutinin (HBHA) is a surface protein involved in epithelial attachment and extrapulmonary dissemination of Mycobacterium tuberculosis. HBHA is attracting increasing attention for its vaccine and diagnostic potential. In a longitudinal study, we investigated non-methylated, recombinant HBHA-specific cytokine and antibody profiles in cohorts of TB patients, their contacts and community controls in an endemic setting. Whole blood assay was done at baseline, 6 and 12 months in patients and contacts, and at entry in controls. ELISA was used to measure IFN-γ, TNF-α and IL-10 (from supernatants), and IgG, IgM and IgA (from sera). Fifty-three percent of controls and 72.1% of contacts were QFT-GIT positive. Baseline IFN-γ was significantly higher in community controls and contacts compared to untreated TB patients (p<0.0001). Controls had significantly higher IgA and lower IgM compared to both untreated TB patients and contacts (p<0.0001). IL-10 was significantly higher in untreated TB patients compared to contacts and controls (p<0.0001). In treated TB patients, IFN-γ significantly increased (p < 0.0001) whereas IL-10 significantly decreased (p<0.001). This study reports for the first time that anti-HBHA IgA could have the potential as a biomarker of protective immunity. In addition, non-methylated, recombinant HBHA-induced IFN-γ could be used as a biomarker of protective immunity and latent TB.