Background Atypical haemolytic uraemic syndrome (aHUS) accounts for ∼10% of all cases of HUS and is often due to complement dysregulation. The short-term outcomes for this disease are established, but there are limited long-term data. The long-term outcomes of a comprehensive nationwide cohort of children with aHUS are presented here. Methods The Australian Paediatric Surveillance Unit prospectively collected data on all cases of HUS in children seen by paediatricians between 1994 and 2001. Patients with aHUS were followed-up with a written questionnaire to the treating clinician at 1 year and again before transition to adult services or at last known follow-up. Results There were 146 reported cases of HUS, of which 14 were aHUS. Ten children required dialysis at first presentation, including two who died and three who did not recover renal function. The disease was relapsing in all but one who survived the presenting episode, with most relapses occurring in the first 12 months. At 1 year, one child was lost to follow-up. Nine of the remaining 11 patients were dialysis dependent. Thirteen kidneys were transplanted into eight children. There was disease recurrence in eight kidneys, which resulted in graft loss in seven. There were three further deaths 1.7, 6.7 and 16.1 years after the initial presentation. Five children developed neurological complications and two had cardiac complications, largely at the time of onset of the disease. Conclusions aHUS is a rare but devastating disease with very high mortality and morbidity that extends beyond the initial presentation period.