We evaluated immunohistochemically the expression profiles of metastasis-associated protein (MTA) 1 and their associations with lymph node metastasis in tonsil cancer. Immunohistochemical analysis of 43 tonsillar neoplasm tissues was performed using antibodies raised to MTA1. Depth of tumor invasion, lymph node metastasis, and clinical outcomes were assessed. Clinical N0 patients were divided into two groups: N0a, negative for MTA1; N0b, positive for MTA1. Occult node metastasis was reevaluated according to the revised clinical N staging system taking account of MTA1 expression. The expression rate of MTA1 was 41.9%. There was a significant correlation between the expression of MTA1 and lymph node metastasis (P = 0.034*). MTA1 had a sensitivity of 53.3% and a specificity of 84.6% for identification of cervical metastases. When cN0b patients were considered to be N+, the recalculated rate of occult metastasis fell from 50% to 7.6% (the false-positive rate remained unchanged). MTA1 was found to be a useful molecular marker to predict lymphatic metastasis in tonsil cancer.