Background: Although there have been recent advances in treatment of colorectal cancer, microarray technology has the potential to improve the application of these therapies by interrogating tumor-specific molecular "fingerprints." Methods: The future applications and benefits of gene expression profiling are discussed. Results: Potential uses include determining who will benefit from chemotherapy, further classifying patients into responders and nonresponders, predicting apoptotic response, developing classifiers to recognize chemosensitive tumors, identifying genes that portend a poor prognosis, revealing genes associated with metastases, predicting the outcome according to clinical stage, and avoiding surgery in patients who would not benefit from resection. Conclusions: Recent research has been aimed at not only finding new molecularly targeted agents, but also identifying specific signatures to predict sensitivity and resistance to therapy. Future care may soon incorporate the data derived from a single microarray chip or similar technology that will describe a patient's tumor, predict prognosis, and direct specific therapy.