We have analyzed the karyotypes of a series of 16 cell lines derived from human squamous cell carcinomas of the head and neck. When the cell lines were grouped according to their in vitro response to radiation, it was observed that some recurrent chromosomal changes occurred with differing frequencies between groups. Radiation resistance was associated with clusters of breakpoints in bands 1p22, 3p21, and 8p11.2 and deletion of distal 14q, while relative radiation sensitivity was associated with a high frequency of breakpoints in 11q13 and duplication of distal 14q. The regions identified point to the possible locations of genes involved in the response to radiation and could provide a series of markers with which to predict response to radiation therapy.