We studied the induction and removal of UV-induced cyclobutane pyrimidine dimers (CPDs) in the ribosomal RNA genes (rDNA) in cultured hamster and human cells. In these genes, which are transcribed by RNA polymerase I, we found no evidence for transcription-coupled repair. The induction of CPDs was heterogeneous in rDNA due to nucleotide sequence: it was lower on the transcribed strand than on the nontranscribed strand and slightly lower in the coding region than in the nontranscribed spacer. Nevertheless, no dramatic difference in CPD induction was observed between rDNA and the dihydrofolate reductase (DHFR) gene. In Chinese hamster ovary cells, we observed no removal of CPDs from either rDNA strand within 24 h after UV irradiation. In these experiments, we did observe efficient repair of the transcribed, but not the nontranscribed, strand of the DHFR gene, in agreement with published results. In human cells, repair of rDNA was observed, but it showed no strand preference and was slower than that reported for the genome overall. No significant differences in repair were observed between restriction fragments from transcribed and nontranscribed regions or between growth-arrested and proliferating human cells, with presumably different levels of transcription of rDNA. We conclude that the modest level of rDNA repair is accomplished by a transcription-independent repair system and that repair is impeded by the nucleolar compartmentalization of rDNA. We discuss the possibility that recombination, rather than repair, maintains the normal sequence of rDNA in mammalian cells.