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Lymph node metastasis is an important factor in determining the outcome of colorectal cancer. If we can predict the presence of lymph node metastasis before surgery, it may help in deciding the need for surgical lymph node dissection or additional preoperative treatment modalities that might improve survival. Our objective here was to identify a set of discriminating genes that can be used for characterization and prediction of lymph node metastasis.Eighty-nine colorectal cancer patients were studied. Gene expression profiles of cancer were determined by human U133 Plus 2.0 GeneChip®, and patients with and without lymph node metastasis were compared.We identified 73 novel discriminating genes in which expression was significantly different between patients with and without lymph node metastasis. Using this gene set, we were able to establish a new model to predict the presence of lymph node metastasis with an accuracy of 88.4%. Discriminating genes were associated with various functions, including receptor activity and transcription regulatory activity. The list of genes included transmembrane glycoprotein, which has been reported to have a close relationship with lymph node metastasis in prostate cancer. Transmembrane glycoprotein showed significantly higher expression in patients with lymph node metastasis.The present study suggests the possibility that gene expression profiling may be useful in predicting the presence of lymph node metastasis. Thus, gene expression profiling could help to establish individualized tailored therapy for colorectal cancer and provide insights into the development of novel therapeutic targets.