Microtubules are important cytoskeletal elements that have been shown to play a major role in many cellular processes because of their mechanical properties and/or their participation in various cell signaling pathways. Nocodazole is used as an effective microtubule-disrupting agent, and many recent studies have used it for the activation of spindle checkpoint. In this study, we sought to identify the potential nocodazole target genes by profiling the gene expression pattern in HeLa cells. When treated with 0.1ug/ml of nocodazole, cells were efficiently arrested in the mitotic phase. HeLa cells also showed a higher proportion of apoptosis after drug treatment for a prolonged period. By DNA chip assay, we discovered that 50 genes changed their expressions in the nocodazole-treated cells with a minimal 2.0-fold change at 18h post-treatment. The majority of the differentially expressed genes belonged to two functional groups--genes involved in transcription regulation and in cellular signaling. These observations could have significant implications for our understanding of the physiological and pathophysiological regulation of spindle disrupting agents in human cells.