Background Lymphoedema distichiasis syndrome (LDS) is an autosomal dominant inherited form of lymphoedema, typically presenting with lower limb lymphoedema from puberty and distichiasis from birth. For up to 97% of patients, a coding change in FOXC2 is identifiable. However, a number of case studies identifying structural variants (SVs) outside of the FOXC2 locus have been reported. Methods Using a range of approaches, including genome sequencing, we investigated whether we could identify SVs, which may be impacting FOXC2 in a series of unsolved cases. In silico tools were used to annotate these variants for potential insights into regulatory mechanisms. Results We identified five families with SVs impacting FOXC2 . One with a mosaic deletion causing a truncated protein, and four with SVs impacting the non-coding portion of the genome downstream of FOXC2 , likely causing dysregulation of the gene. A review of 28 patients in the DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources (DECIPHER) database with 16q24 deletions, including the whole of FOXC2 , identified only two reported to have lymphoedema or distichiasis. Conclusion These additional cases bolster the evidence supporting FOXC2 as a monogenic cause of LDS. The fact that these SVs are not detected through panel testing underscores the recommendation for employing genome sequencing or array-comparative genomic hybridisation (CGH) in patients with suspected LDS who lack a genetic diagnosis. Public databases of patients with 16q24 deletions, incorporating FOXC2 , but without lymphoedema reported, demand caution when interpreting deletions affecting the entirety of FOXC2 . Work is required to explore the role of these putative regulatory elements whose dysregulation may cause this syndrome.