Genotoxicity is a collective term that includes any process which affects the integrity of genomic DNA. With regard to gene therapy, the insertion of genetic elements and the expression of DNA-modifying proteins are the main mediators of genotoxic side effects. The practicability of gene-addition-type gene therapy protocols has been demonstrated in several successful clinical trials, but the risk of insertional mutagenesis remains a major obstacle. Targeted strategies aimed at correcting a mutation directly in the genome can preserve temporal and tissue-specific expression of the afflicted gene. However, sufficient gene targeting frequency can only be achieved upon expression of tailor-made nucleases. Partly because of insufficient specificity, such designer nucleases can challenge genome integrity. Here, the origin and the consequences of genotoxicity are reviewed, with a focus on assays that have been developed to assess genotoxicity. In addition, approaches to reduce toxicity associated with the major gene therapy strategies are discussed.