In total 33/421 childhood cancer were diagnosed in the FA population compared to expected 0.74 (SIR = 39; 95% CI, 26–56). The highest cancer risk were observed in patients with biallelic mutations: FANCD1 (BRCA2; SIR = 324; 95% CI, 88–830) or FANCN (PALB2; SIR = 422; 95%CI, 51–1526), while no neoplasms were observed in patients (n = 20) with biallelic mutations: FANCD2. The cumulative cancer risk before age 18 years was 10.6% in the entire FA cohort. Here, FANCD2 is linked to childhood malignant neoplasm.