The majority of complement factor H mutations associated with atypical hemolytic uremic syndrome (HUS) are heterozygous. Homozygous mutations causing atypical hemolytic uremic syndrome are rare. We report a 7-month-old boy with HUS, severe hypocomplementemia (low C3 and normal C4 levels), and extremely low circulating levels of factor H. Genetic analysis showed homozygous 4 bp deletion in the gene encoding factor H in the patient, with his parents being carriers. The patient showed progression to end-stage renal disease and is presently on chronic ambulatory peritoneal dialysis.