The loss of chromosome Y has often been observed in human solid tumors. This chromosome aberration has been proposed as one of genetic changes predisposing men to squamous cell carcinoma of the head and neck (SCCHN). In this study, using cytogenetic analysis and fluorescence in situ hybridization we analyzed: 16 cell lines derived from primary and recurrent SCCHN, a group of 22 samples derived from of previously analyzed primary larynx tumors and their corresponding metastases and a group of eight multiple primary tumors received from two different locations within the head and neck region of the same patients.In the majority of analyzed cell lines we found both loss of chromosome Y and SRY-probe signals (68.7% of samples) and these were nearly always found in the analyzed metaphases. The whole chromosome Y was usually lost, but in two cases we observed translocation of this chromosome to chromosomes 1, 3 and 17.Among all primary tumors, 14 (63.6%) and 15 of their metastases (68.2%) showed a loss of chromosome Y in a prevailing number of analyzed nuclei. Also, in the group of primary tumors and second primary tumors, all samples had a loss of the chromosome Y in the majority of analyzed nuclei.