The majority of classical tumor suppressor genes, such as CDKN2A or RB1, were identified by delineation of biallelic losses called homozygous deletions. To systematically identify homozygous deletions in laryngeal squamous cell carcinoma and to unravel novel putative tumor suppressor genes we screened three laryngeal squamous cell carcinoma cell lines (LSCC) using array comparative genomic hybridization (array-CGH). Out of 31 candidate regions for homozygous deletions identified by array-CGH, 5 were verified further by PCR. Among others, these homozygous deletions affected the tumor suppressor gene CDKN2A and the apoptosis-inducing STK17A gene. To assess the frequency of the identified deletions we investigated the affected sites in 9 additional LSCC cell lines. In 5 of the 9 cell lines the CDKN2A gene was homozygously lost. Thus, CDKN2A was homozygously deleted in 7 of the 12 cell lines. No other recurrent homozygous deletions were found. Homozygous deletions was a frequent mechanism of CDKN2A inactivation. Moreover, we identified several other genes, including the putative tumor suppressor gene STK17A, which may be inactivated by homozygous deletions and thus are potentially implicated in laryngeal squamous cell carcinoma development.