Background This study was designed to detect methylation of E-cadherin gene promoter and gene mutation of β-catenin in exon 3 and their expression of protein and mRNA in primary tumor and lymph node metastatic tumor of nasopharyngeal carcinoma (NPC), and investigate the mechanism of invasion and metastasis of neoplastic cells in NPC Methods Fourty-two fresh biopsy samples were taken from untreated NPC patients at the Affiliated Hospital of Sun Yat-sen Medical College, Sun Yat-sen University, Guangzhou, China during the period of 1999-2002 Among them 21 were taken from primary tumors and the other 21 from lymph node metastatic tumors The gene promoter methylation of E-cadherin was detected by methylation-specific PCR (MSP) The mutation in exon 3 of β-catenin was detected by direct sequencing analysis RT-PCR, Western blot and immunohistochemical staining were used to detect the mRNA and protein expression patterns in both primary and metastatic tumors of NPC Results Down-regulated expression of E-cadherin in metastatic tumor was compared with that in primary tumor Reduced expression of E-cadherin was found to be correlated with lymph node metastatic tumor of NPC ( P =0 004); but there was no obvious correlation between primary and metastatic tumors in the expression of β-catenin ( P =0 698) The mRNA expression level of E-cadherin in metastatic tumors decreased significantly compared with that in primary tumors However, little change was observed in the mRNA level of β-catenin in different tumor tissues Only 4 samples (19 1%) displayed gene promoter methylation of E-cadherin in primary tumor and 10 samples (47 6%) showed methylated form of E-cadherin The gene promoter methylation of E-cadherin was more common in metastatic tumor than in primary tumor of NPC ( P =0 024) Only 2 (4 76%) of the 42 samples showed mutations in exon 3 of β-catenin at 41 (T41A, ACCGCC) and codon 47 (S47T, AGTACT) The cytoplasmic and nuclear expression of β-catenin in tumor was not found in any samples of NPC Conclusions The results suggest that the downregulation of E-cadherin results from the gene promoter aberrant methylation of E-cadherin and that the methylation of E-cadherin plays an important role in invasion and metastasis of tumor cells in NPC However, β-catenin mutation is an infrequent event in NPC, and β-catenin is not a critical factor influencing the invasion and metastasis of tumor cells in NPC Background This study was designed to detect methylation of E-cadherin gene promoter and gene mutation of β-catenin in exon 3 and their expression of protein and mRNA in primary tumor and lymph node metastatic tumor of nasopharyngeal carcinoma (NPC), and investigate the mechanism of invasion and metastasis of neoplastic cells in NPC Methods Fourty-two fresh biopsy samples were taken from untreated NPC patients at the Affiliated Hospital of Sun Yat-sen Medical College, Sun Yat-sen University, Guangzhou, China during the period of 1999-2002 Among them 21 were taken from primary tumors and the other 21 from lymph node metastatic tumors The gene promoter methylation of E-cadherin was detected by methylation-specific PCR (MSP) The mutation in exon 3 of β-catenin was detected by direct sequencing analysis RT-PCR, Western blot and immunohistochemical staining were used to detect the mRNA and protein expression patterns in both primary and metastatic tumors of NPC Results Down- regulated expression of E-cadherin in metastatic tumor was compared with that in primary tumor Reduced expression of E-cadherin was found to be correlated with lymph node metastatic tumor of NPC (P = 0 004); but there was no obvious correlation between primary and metastatic tumors in the expression of β-catenin (P = 0 698) The mRNA expression level of E-cadherin in metastatic tumors decreased significantly compared with that in in primary tumors However, little change was observed in the mRNA level of β-catenin in different tumor tissues Only 4 samples (19 1%) displayed gene promoter methylation of E-cadherin in primary tumor and 10 samples (47 6%) showed methylated form of E-cadherin The gene promoter methylation of E-cadherin was more common in metastatic tumor than in primary tumor of NPC (P = 0 024) Only 2 (4 76%) of the 42 samples showed mutations in exon 3 of β-catenin at 41 (T41A, ACC  GCC) and codon 47 (S47T, AGT  ACT ) The cytoplasmic and nuclear ex pressionof β-catenin in tumor was not found in any samples of NPC Conclusions The results suggest that the downregulation of E-cadherin results from the gene promoter aberrant methylation of E-cadherin and that the methylation of E-cadherin plays an important role in invasion and metastasis of tumor cells in NPC However, β-catenin mutation is an infrequent event in NPC, and β-catenin is not a critical factor influencing the invasion and metastasis of tumor cells in NPC