Atypical Haemolytic Uraemic Syndrome (aHUS) is a thrombotic microangiopathy that often provokes irreversible renal damage and post-transplantation recurrence. Studies performed during the last decade have shown that 50-60% of aHUS patients present genetic or acquired defects in the complement system that enhance the initial endothelial damage and favour disease development. This review analyses the complement proteins and processes that are disturbed in aHUS patients, and outlines the relevance of a prompt genetic/molecular diagnosis for improving clinical management and prognosis.