The attenuated Mycobacterium tuberculosis strain H37Ra is one of the most commonly used controls for M. tuberculosis identification in the clinical laboratory and is a source of false-positive results for M. tuberculosis as a consequence of cross-contamination. Therefore, the ability to discriminate between H37Ra and real clinical isolates has important public health implications. To date, differentiation of H37Ra from M. tuberculosis clinical isolates is possible only by IS6110 genotyping and spoligotyping. In the 1950s, some authors reported that the virulent strain H37Rv and M. tuberculosis clinical isolates were able to fix basic dyes in their anionic forms, while H37Ra was not. We have studied the different techniques described for M. tuberculosis cytochemical staining and have chosen the best of these, introducing certain modifications in order to increase their discriminative power and reproducibility. We describe cytochemical staining of M. tuberculosis cells with neutral red and Nile blue, which differentiates H37Ra from virulent strains. This method could be used as an easy laboratory tool for distinguishing between H37Ra and real M. tuberculosis clinical isolates.At present, Mycobacterium tuberculosis identification is normally carried out in clinical laboratories by using conventional tests such as niacin, nitrate reduction, pyrazinamidase, thiopen-2-carbonic acid hydrazide (TCH), or catalase (13,21,22). In addition, the M. tuberculosis complex can be distinguished from other mycobacteria by commercialized nucleic acid probes (20) and high-performance liquid chromatography analysis of mycolic acid (4). However, it is not possible to distinguish the attenuated strain H37Ra from M. tuberculosis clinical isolates by use of these techniques. Nevertheless, H37Ra is used as a control in identification tests, and false diagnosis of tuberculosis due to cross-contamination of laboratory specimens with H37Ra is both likely and frequent (3,16). To date, reliable differentiation of H37Ra from virulent strains has been possible only through spoligotyping and IS6110 genotyping (1), laborious and time-consuming procedures.Cytochemical reactions in tubercle bacilli were studied in great depth in the 1940s and 1950s in order to find phenotypic markers correlated to virulence. The action of many basic dyes, such as Nile blue, methylene blue, neutral red, and methyl violet, on different Mycobacterium strains has been studied (5,6,7,8). The most successful results were obtained with neutral red and Nile blue (6, 8). Dubos and Middlebrook reported that H37Rv, together with 22 M. tuberculosis and Mycobacterium bovis isolates, fixed neutral red in an alkaline aqueous environment and became red in color, whereas H37Ra cells did not (8). Two subsequent studies in which larger numbers of M. tuberculosis clinical isolates were used (about 200 strains in each) corroborated these findings (11,15). At the same time, Desbordes and coworkers concluded that, unlike attenuated and avirulent strains, the virulent strain H37Rv strongly...