To examine whether genetic factors influence the prognosis of cancer patients, several microsatellite markers were used to determine the allelic loss of certain areas of the genome. Three microsatellite markers, D3S1067, IFNA and D9S171 were used to study the loss of heterozygosity (LOH) of 3p21 and 9p21 in 93 head and neck squamous cell carcinomas. Of 57 informative cases, LOH was detected in 27 of 57 (47%) DNA samples obtained from cancer specimens when at least one marker was used. The frequency of LOH was not correlated with the clinical factors. However, the frequency of LOH was significantly higher in the recurrent cases than in the non-recurrent cases, and patients with 3p21 and/or 9p21 LOH tended to survive for a shorter period of time. These results suggested that the allelic loss at 3p21 and/or 9p21 could be correlated with the prognosis of the patients, and that it was a novel prognostic factor independent of other clinical factors concerning head and neck cancers. LOH at 3p21 and/or 9p21 may help to identify head and neck cancer patients with a poor prognosis, who need an intensive postoperative follow-up protocol, or who are suitable for novel investigational therapeutic approaches.