The spindle checkpoint monitors the fidelity of chromosome separation during mitosis. Aberrations in key regulators of this process have been found in human malignancies associated with chromosomal instability (CIN). Important chemotherapeutic agents which alter microtubule dynamics such as paclitaxel and vincristine, prolong spindle checkpoint activation and delay the completion of mitosis. Intriguingly, inhibition of BubR1 or overexpression of Aurora kinase A, spindle checkpoint regulators implicated in CIN, promote resistance to microtubule inhibitors (MTIs) in vitro. Taxanes have failed to demonstrate significant clinical benefit in phase II trials in colorectal cancer (CRC). The high incidence of CIN in this disease, coupled with alterations in spindle checkpoint regulators in vivo, may explain the disappointing results associated with taxane based therapies for CRC. A phase II trial of taxanes in patients with metastatic CIN negative CRC may be indicated.