Pycnodysostosis is a rare genetic disease. Impaired osteoclastic function is the basis for typical phenotypic features and bone fragility. The main differential diagnosis is osteopetrosis, also associated with altered bone remodelling, but with a more severe prognosis. We describe the case of an 8-year-old boy who presented life-threatening obstructive sleep apnoea successfully managed with non-invasive ventilation. Haematological overlap phenotype included anaemia and altered bone marrow, more common in osteopetrosis. Molecular analysis of the CTSK gene revealed a mutation not previously described in the literature.