The objective of this study is to describe the molecular alterations in carcinomas in one specific location of the head and neck, the hypopharynx. Thirty-seven hypopharyngeal squamous cell carcinomas were studied. The DNA from tumour and healthy tissue was evaluated for amplification of the 11q13 region and of the MYC and ERBB1 oncogenes, for integration of the Human Papillomavirus (HPV), and for loss of heterozygosity (LOH) at p53 and NAT2 loci. The most common alteration was the amplification of the 11q13 region (78% of the cases), followed by LOH at p53 locus (70%). MYC amplification was found in 19% of the cases, ERBB1 amplification in 29%, LOH at NAT2 locus in 25%, and integration of the HPV in 29%. 11q13 amplification was related with nodal metastases and higher tumour recurrence rates. These findings confirm that 11q13 amplification is one of the most frequent genetic alterations in hypopharyngeal squamous cell carcinomas, and that it may have prognostic significance in these tumours.