We have observed reactive scattering damage to fundamental DNA building blocks by the type of hyperthermal secondary ions that are produced along heavy ion tracks in biological media. Reactions include carbon abstraction by N+, and hydrogen abstraction by O− and N+, at collision energies down to 1 eV. Our results show that localized reactive scattering by hyperthermal secondary fragments can lead to important physicochemical damage to DNA in cells irradiated by heavy ions. This suggests a fundamentally different picture of nascent DNA damage induced by heavy ion tracks, compared to conventional (x or γ) radiation tracks.