We have measured gene-specific DNA damage and repair of alkaline-sensitive sites and DNA strand breaks after gamma-irradiation. Although fairly high doses are used in order to introduce sufficient DNA damage, Foe find that there is efficient and almost complete repair within 2 h. Human colon cancer cells were exposed to gamma-irradiation, and the repair was measured in various nuclear regions and in the mitochondrial genome. In the essential housekeeping gene, dihydrofolate reductase (DHFR), there was about 80% repair of the strand breaks after 2 h. There was no difference in the repair activities between the two individual DNA strands of the DHFR gene, and thus no evidence of strand bias, or transcription coupling of the repair process. There was no preferential repair of the DHFR gene compared to repair in an inactive, X-linked, noncoding gene. We can thus not detect any nuclear heterogeneity of the formation and repair of these lesions. In contrast, the formation and processing of gamma-irradiation introduced lesions differ in the mitochondrial DNA. Here, we detect about twofold more alkaline-sensitive sites and strand breaks after gamma-irradiation than observed in the DHFR gene. The repair of these lesions is deficient in the mitochondria, where only about 25% are removed within 2 h.