The mutant allele-specific amplification (MASA) method is capable of detecting one tumor cell containing genetic changes in a sample containing thousands of normal cells. To investigate whether MASA can be applied to sensitive detection of lymph node metastasis, we screened 22 colorectal cancers for K-ras and p53 mutations and examined corresponding regional lymph node at the genetic level by the MASA method. Six of the primary tumors were found to certain K-ras mutations, and nine exhibited mutations of the p53 gene. In seven of the 14 cases in which genetic alterations were identified (mutations in both genes were found in one tumor), we found discrepancies between the genetic and the histopathological diagnoses with respect to the presence or absence of cancer cells in lymph nodes, in that these patients were histologically diagnosed lymph node negative, hn(-) but genetically diagnosed lymph node positive, gn(+). Because disease recurs in 20–30% of cancer patients whose lymph nodes are histopathologically negative after surgery, genetic evaluation of lymph nodes for metastasis may become a useful prognostic indicator.