We describe a 4-month-old child who developed unusual thrombotic complications following allogeneic BMT for Omenn syndrome, a form of SCID. Eight weeks after the procedure the child suffered a major cerebrovascular accident and developed acute pulmonary hypertension in association with persistently elevated anticardiolipin antibody titres. It is postulated that central line-derived microemboli caused these serious thrombotic complications in the context of an evolving hypercoaguable state.