Loss of tumor suppressor genes and apoptosis-associated genes was common event in laryngeal squamous cell carcinoma (LSCC). Apaf-1 (apoptotic protease activating factor-1) is a key factor in cytochrome C-dependent apoptotic pathway. To investigate the effect of Apaf-1 in progression of LSCC, we analyzed Apaf-1 from DNA and RNA levels. Semi-quantitative RT-PCR analysis of Apaf-1 mRNA showed that over 40 percent of LSCCs (11/27) were low expression compared to the para-neoplastic laryngeal tissues (PNTs). The results of CGH indicated loss in 2 of 18 cases but no amplification on chromosome 12q22-23. The LOH frequencies of D12S327, D12S1657, D12S393, D12S1706, D12S346 on 12q22-23 were 18.2%, 13.6%, 18.2%, 22.2% and 16.6%, respectively in 72 matched samples of LSCCs and PNTs. Methylation-specific PCR displayed that all of 11 LSCCs, whose expression of Apaf-1 mRNA down-regulated, were methylated in promoter regions. In contrast, only 1 of 16 LSCCs with no changes in Apaf-1 mRNA levels was methylated (chi2 test, P=0.0001). The results implied that abnormal expression of Apaf-1 participates in the genesis of LSCCs and decreased expression of Apaf-1 mRNA were not mainly due to the deletion of Apaf-1 gene. The Apaf-1 DNA methylation in promoter region might contribute to the decreased transcription of Apaf-1 in LSCCs.