A growing number of sequenced genomes belonging to the Mycobacterium tuberculosis complex has enabled a comparison of strain traits and genomic constitution. These analyses may reveal mechanisms of evolution and genomic variation relevant to tuberculosis pathogenesis.Multiple alignments were used to analyze the differences between six genomes of the M. tuberculosis complex and to locate regions of variation that may lead to improvements in species identification or in their treatment.The Mauve software package was used to perform a multiple alignment of 6 genomes belonging to the M. tuberculosis complex. Regions exclusive to each genome were annotated using the TB database.Percent similarity among the six genomes ranged between 96.1% and 97.8%. The annotation identified intergenic regions, regions associated with transposable elements of the PE-PGRS and PPE families, and regions associated with resistance against bacteriophage.In spite of the high genetic similarity among the tuberculosis strains, genomic variations were elucidated that may be relevant to differences in behavior and virulence, as well as for improvement of strain diagnosis. Regions encoding membrane-associated proteins, possibly related with antigenic variation and immune response, are particularly interesting for studies aimed at seeking tuberculosis treatments.