To determine whether inactivation of the p16 gene mapped to the chromosome 9p21 region is associated with the development of oral squamous cell carcinoma (SCC), we investigated the mutational states of two forms of alternative transcripts (alpha and beta) from the p16 gene in 14 oral SCC cell lines by means of RT-PCR, PCR, direct sequencing and methylation analyses. Alterations of the alpha transcript were detected in all of the cell lines examined: homozygous deletions in three lines; subtle mutations in exons 1 alpha or 2 in four lines; skipping of exon 2 in two lines; hypermethylation of the 5' CpG island of the p16 gene in four lines; and an unknown mechanism in one line. On the other hand, abnormalities of the beta transcript were observed in seven of the 14 cell lines. Nonetheless, the mutations that essentially affect the function of the encoded protein were found only in five cell lines, including three lines with homozygous deletion. There was no cell line having only beta transcript alterations. Thus, alteration of the alpha transcript of the p16 gene was a highly frequent event in oral SCC. Since this type of alteration resulted in gene inactivation through multiple pathways, it may play a major role in the process of oral SCC development.