Microtubules are still a promising target for new therapeutic agents. Thus, there is a continuous interest for compounds able to modify microtubule assembly, either by interacting directly with tubulin, or by interacting with microtubules regulators. Because of its dynamic characteristics, the microtubule cytoskeleton is a suitable target for small molecules that rapidly diffuse in the cell cytoplasm. Moreover, compounds targeting the microtubule cytoskeleton have proved to be valuable tools for basic research in cell biology. In this paper, after a short presentation of the apparent molecular pathways involved in the anticancer effect of agents that interfere with microtubules functions, the potentials and impact of chemogenomics and cell-based assays in the discovery of new therapeutic compounds and of new regulators of the microtubule cytoskeleton are described.