We identified a unique deletion encompassing exons 6–31 of the FANCA gene in an eight‐year‐old girl with Fanconi anaemia (Patient 16; Table 2; Figure S1) and a novel mutation in the non‐homologous end joining factor 1 gene (NHEJ1, also termed Cernunnos) (Patient 17; Table 2). Here, NHEJ1 is linked to Fanconi anemia.