Haemolytic uraemic syndrome (HUS) is most commonly associated with Shiga toxin-producing Escherichia coli (STEC) while the recurrent hereditary atypical (aHUS) form secondary to complement system control protein mutations is relatively rare. A 6-year-old boy with complement factor H (CFH) and factor B (CFB) mutations and a history of bloody diarrhoea and PCR positivity for Shiga toxin was initially diagnosed as STEC+HUS. Acute kidney injury resolved with Eculizumab but he remains with chronic renal failure. Although the exact role of STEC in the pathogenesis of aHUS in this patient is not certain, there seems to be a relationship. However, several issues remain to be explained including the effect of genetic and environmental factors in modifying susceptibility to develop aHUS in some patients following STEC infection.