Mycobacterium tuberculosis gene expression studies have involved "in vitro", "ex vivo" and "in vivo" experiments (animal models), but without the expected success. We propose that key features of human tuberculosis could be discovered by studying the M. tuberculosis gene expression within the human host. Therefore, we isolated totalM. tuberculosis mRNA from human clinical respiratory specimens of patients diagnosed with pulmonary tuberculosis; after this, we synthesized the dscDNA and tested it by qualitative RT-PCR assays. We detected the expression of IS6110 insertion sequence and of the "housekeeping" genes 16SrRNA andsigA in M. tuberculosis grown in vivo (pulmonary tuberculosis) as well as grown in vitro M. tuberculosis. mprA and mprB genes expression, which code the MprAB signal transduction system, were only detected in M. tuberculosis grown in vitro. Our results provide the first step towards a non invasive methodfor the study of the transcriptome of M. tuberculosis within its native host, to analyze "in vivo" regulation of the genetic determinants required for virulence and pathogenesis.