Introduction: The sputum smear or the culture are the definitive diagnosis of pulmonary tuberculosis. Only a fraction of clinical patients are culture-confirmed. Methodology: A total of 24 clinical cases (40 ± 14 years old) with positive smear and negative co-morbidity were studied. Cases were selected from 600 patients who attended the pneumology service over two years. A sputum sample was cultured in Löwenstein-Jensen medium with consequent amplification of the rrnA V2 promoter, the differentiation region 4, and the IS6110 insertion sequence of Mycobacterium tuberculosis. After the culture result, the patients were divided into negative (n = 14) or positive (n = 10) culture groups. In addition, 30 samples from healthy donors (45 ± 10 years) were studied. The numbers of CD4, CD8 and CD19 lymphocytes were determined by flow cytometry. Levels of IgA and IgG to M. tuberculosis were measured by ELISA. Results: IgG and IgA levels were detected in patients with positive culture, while only IgA was found in patients with negative cultures. The lymphocyte populations in the two groups were similar.  The presence of a pleural apical cap was found more frequently in patients with negative- (57%) than with positive cultures (10%). Conclusions: The isotype profile in patients with positive cultures was both IgA and IgG positive, while in patients with negative culture, only IgA was found. The results will contribute to improve the diagnostic algorithm and appropriate treatment of patients with clinical tuberculosis. Further studies are needed to determine if this profile is predictive of the outcome of isolation.