It is known that a combined glycine/lysozyme treatment is able to induce in vitro the mycobacterial conversion from the bacillary to the cell wall defective forms. These forms also naturally occur in vivo as a response to various antimicrobial factors such as lysozyme released by phagocytic cells. Although they have been successfully isolated from patients with several chronic diseases, their role in pathogenesis is still unknown, mainly due to the difficulties in handling the in vivo isolated variants. Moreover, nothing is known about the transcriptional peculiarities that may exist in comparison to the vegetative phase. Hence, in this study, we simulated in vitro the induction of the mycobacterial cell wall defective state by using a glycine and lysozyme-based treatment in order to identify the gene expression profiles of both pathogenic and non-pathogenic mycobacteria. DNA-microarray results showed that in contrast to the non-pathogenic Mycobacterium smegmatis species, glycine and lysozyme treated forms of Mycobacterium tuberculosis and Mycobacterium avium subspecies paratuberculosis regulated a repertoire of genes usually expressed in vivo during adaptation and persistence within host environments. Results suggest that the cell wall defective state may represent an important stage in the life-cycle of pathogenic mycobacteria that potentially coordinates persistence.