The efficiency of DNA single-strand break induction was measured in transcriptionally active DNA, transcriptionally inert satellite DNA, and bulk DNA sequences of mouse L929 cells using the alkaline filter elution assay. The cells were exposed to increasing doses of X-radiation up to 1000 rad. DNA which either eluted from or was retained on polycarbonate filters during the assays was collected onto nitrocellulose filters and hybridized against radiolabeled poly(A+)RNA (to probe transcribing DNA sequences) or mouse satellite DNA. The increasing rate and extent of elution of bulk DNA or specific DNA sequences after increasing radiation doses was taken as a measure of the increased frequency of radiation-induced DNA strand breaks. The results indicate that a significant fraction of transcriptionally active DNA contains endogenous strand breaks. With increasing dose, the efficiency of radiation-induced DNA strand breakage in bulk, transcriptionally active and satellite DNA sequences was observed to be the same when the sum of all eluted DNA was considered. However, the early eluting fractions contained DNA which was enriched in active sequences. Since DNA elutes as a function of size, the early fractions contain smaller DNA than later fractions. Therefore, our results indicate that the fraction of active sequences which elutes early resides on smaller fragments on the average than the later eluting DNA, and that even low doses of radiation preferentially cause breaks in regions of DNA containing active sequences.