An estimated one third of tuberculosis (TB) cases go undiagnosed or unreported. Sputum samples, widely used for TB diagnosis, are inefficient at detecting infection in children and paucibacillary (smear negative) patients. Indeed, developing point-of-care biomarker-based diagnostics that are not sputum-based is a major priority for the WHO. Here, we tested exhaled breath condensate (EBC) for Mycobacterium tuberculosis (Mtb) molecules and assessed whether this approach allows pulmonary TB diagnosis. Mtb-specific lipids, lipoarabinomannan lipoglycan, and proteins present in EBCs unambiguously differentiate TB patients from controls. We used EBCs to track the longitudinal effects of antibiotic treatment in Mtb-infected children. In addition, Mtb lipoarabinomannan and lipid structure in EBC revealed specific metabolic and biochemical states of Mtb in the human lung. Our data collectively indicate that EBC analysis can unequivocally diagnose TB across all patient populations and monitor treatment efficacy. This affordable, rapid and non-invasive approach seems superior to sputum assays and can potentially easily be implemented at point-of-care.