We present a child with Fanconi anaemia and congenital hypopituitarism, who developed intracerebral calcifications, progressive spasticity and retinopathy. The chromosome fragility with mitomycin C was increased in both the patient and his sibling, confirming a diagnosis of Fanconi anaemia. Aplastic anaemia in association with intracerebral calcifications has been described in patients with dyskeratosis congenita and Revesz syndrome, but not so far in confirmed cases of Fanconi anaemia. This case further illustrates the greater overlap of associated features in congenital bone marrow failure syndromes. It also indicates that Fanconi anaemia should be actively excluded where such associated features are found.