There has been a substantial investment in elucidating the mechanism of expansion in hopes of identifying therapeutic targets for Huntington disease (HD). Although an expanded CAG allele is the causal mutation for HD, there is evidence that somatic expansion may not be the only disease driver. We report here that double strand breaks (DSBs) drive HD toxicity by an independent mechanism from somatic expansion. The mutant HD protein inhibits non-homologous end joining (NHEJ) activity, leading to the accumulation of DSBs. DSBs promote transcriptional pathology in mice that cannot expand their CAG tracts somatically. Conversely, Inhibition of DSBs reverses neuronal toxicity in animals that undergo somatic expansion. Although they coexist in neurons, DSBs and somatic expansion are independent therapeutic targets for HD.