Radioactive compounds incorporated in tissues can have biological effects resulting from energy deposition in subcellular compartments. We addressed the genetic consequences of [(3)H] or [(14)C]thymidine incorporation into mammalian DNA. Low doses of [(3)H]thymidine in CHO cells led to enhanced sensitivity compared with [(14)C]thymidine. Compared with wild-type cells, homologous recombination (HR)-deficient cells were more sensitive to lower doses of [(3)H]thymidine but not to any dose of [(14)C]thymidine. XRCC4-defective cells, however, were sensitive to both low and high doses of [(3)H] and [(14)C]thymidine, suggesting introduction of DNA double-strand breaks, which were confirmed by gamma-H2AX focus formation. While gamma rays induced measurable HR only at toxic doses, sublethal levels of [(3)H] or [(14)C]thymidine strongly induced HR. The level of stimulation was in an inverse relationship to the emitted energies. The RAD51 gene conversion pathway was involved, because [(3)H]thymidine induced RAD51 foci, and [(3)H]thymidine-induced HR was abrogated by expression of dominant negative RAD51. In conclusion, both HR and non-homologous end-joining pathways were involved after labeled nucleotide incorporation (low doses); genetic effects were negatively correlated with the energy emitted but were positively correlated with the energy deposited in the nucleus, suggesting that low-energy beta-particle emitters, at non-toxic doses, may induce genomic instability.