Currently the value of oncogenes and tumour suppressor genes as biological markers in the treatment of head and neck cancer squamous cell carcinoma (HNSCC) is being discussed. Previous studies have demonstrated that mutated or overexpressed genes controlling the apoptosis pathway, such as p53 chromosome loss at 9p21 and 11p15 are frequent genetic alterations in these tumours. This study was conducted to investigate, as to whether there is any correlation between genetic markers controlling the apoptotic pathway and clinical outcome. Prior to radiotherapy (XRT) tumour DNA was sampled from 74 HNSCC patients. Leukocyte and tumour DNA were screened by microsatellite analysis of 9p21-22 and 11p15. To determine the frequency of p53 mutations single-strand conformation polymorphism (SSCP) analysis was used. Allelic loss at 9p21 was found in 61% of tumours. The region 11p15 was deleted in 18% of samples. P53 mutations were identified in 20 of 74 patients. Our data confirm a close association of LOH 11p15 with p53 mutations, which has not been described, yet. LOH at 9p21 was associated with histopathological grade and significantly related to overall survival. These data suggest, that genetic markers such as chromosome loss at 9p21 may have potential implications for clinical and prognostic evaluation in HNSCC patients undergoing XRT.