We developed a combined strategy consisting of microarray based comparative genome hybridization (array CGH), high-resolution quantitative PCR (qPCR) and sequencing of CNCs located in the SRO 5′ to FOXL2. Samples from 57 BPES patients who do not carry an intragenic FOXL2 mutation or gene deletion were studied, revealing a distant 7.4 kb deletion as the most prominent finding. The gene discussed is FOXL2; the disease is blepharophimosis, ptosis, and epicanthus inversus syndrome.