Tuberculosis has become one of the deadliest global emergencies due to the widespread existence of multiple drug resistance strains of Mycobacterium tuberculosis and the increase of immuno-compromised populations in large parts of the world. Although the complete genome of M. tuberculosis became available in 1998, opening unprecedented opportunities for target-specific drug development, the progress since then has been slow, mainly due to a lack of a sufficiently strong interest by pharmaceutical and biotechnology industries. One of the most promising tools for future drug discovery lies in the elucidation of the molecular structures of potential drug targets from the M. tuberculosis proteome. During the last five years, the structures of about 200 unique targets have already been determined, which comprise about 5% of the entire M. tuberculosis proteome. As an example, we present the approach and some of the key achievements of the X-MTB consortium based in Germany. We summarize and discuss some recent highlights of potential drug targets of M. tuberculosis involved in lipid metabolism, protein phosphorylation/dephosphorylation and amino acid biosynthesis. The achievements of several structural genomics consortia that focus on targets from the M. tuberculosis proteome are now providing a solid framework to support coordinated international approaches for future structure-based drug discovery programs at the interface between industrial enterprises and academic research. One of the objectives will be to focus on target complexes, in addition to single targets that dominate the present repository of structures from the M. tuberculosis proteome.