Long interspersed nuclear element 1 (LINE-1) is the only autonomous retrotransposon in humans and represents 17% of the genome. LINE-1 retrotransposition occurs by a “copy and paste” mechanism in which an RNA intermediate is reverse-transcribed and integrates at a new genomic location. LINE-1 elements have shaped the evolution of the human genome but are often deleterious causing insertional mutagenesis, transcriptional dysregulation and genomic instability. De novo LINE-1 insertions are frequently pathogenic causing inherited genetic diseases but also contributing to somatic diseases, such as auto-inflammatory and neurological disorders, and tumorigenesis. Therefore, organisms have evolved multiple mechanisms to restrict LINE-1 element expansion. In somatic cells, LINE-1 elements are usually transcriptionally silenced with both DNA methylation and chromatin modification playing critical roles in restricting LINE-1. Germline-specific restriction factors, such as the piRNA, are critical to restrict LINE-1 retrotransposition preventing the acquisition of novel integrations between generations but also to maintain fertility. However, an emerging body of evidence has implicated DNA repair as a new process contributing to both suppressing and promoting LINE-1 retrotransposition. Roles for factors involved in a wide range of repair processes have been implicated using different cell-based assays, from the repair of bulky adducts (factors involved in nucleotide excision repair) to factors required to maintain DNA replication fork stability (BRCA1 and FANCD2). Despite this, two key questions remain to be elucidated; firstly, how does the DNA repair machinery suppress LINE-1 retrotransposition? And secondly, is DNA repair a physiologically relevant LINE-1 restriction mechanism? Here, using reverse genetics, I show that Fanconi Anaemia DNA inter-strand crosslink (FA ICL) repair factors act in concert to restrict LINE-1 retrotransposition. Moreover, by purifying the recombinant FA ICL repair incision complex (SLX4-XPF-ERCC1), I show that it can cleave intermediates of retrotransposition, aborting new integrations. I show that all stages of FA ICL repair, defective in the human disease FA, are required to prevent retrotransposition in vivo. I find that FA ICL repair-deficient mice accumulate LINE-1 integrations in an array of somatic tissues with male germ cells having very high levels of such events. Finally, I find that early zygotic development is particularly dependent upon FA ICL repair factors to prevent LINE-1 retrotransposition.