Atypical hemolytic uremic syndrome is a prototypic thrombotic microangiopathy attributable to complement dysregulation. Hypertensive emergency, characterized by elevation of systolic (>180mmHg) or diastolic (>120mmHg) blood pressure together with end-organ damage, can cause thrombotic microangiopathy which may mimic atypical hemolytic uremic syndrome. We sought to retrospectively evaluate the clinical, biological and complement genetic characteristics of 76 and 61 atypical hemolytic uremic syndrome patients with and without hypertensive emergency, respectively. Patients with hypertensive emergency-hemolytic uremic syndrome were more frequently males, with neurological involvement, and a slightly higher hemoglobin level. At least one complement rare variant was identified in 51.3% (39/76) and in 67% (41/61) patients with or without hypertensive emergency, respectively (p=0.06). In both group, renal prognosis was severe with 23% and 40% of patients reaching end stage renal disease after a 5-year follow-up (p=0.1). The 5-year renal survival was 77% in patients without hypertensive emergency nor complement variant, and below 25% in the three groups of patients with hypertensive emergency and/or complement variant (p=0.02). In patients without hypertensive emergency, 5-year renal survival was 100% vs 40% with or without Eculizumab, respectively (p<0.001). Conversely, the 5-year renal survival of patients with hypertensive emergency was 46% vs 23% with or without Eculizumab, respectively (p=0.18). In conclusion, hypertensive emergency and complement rare variants are essential to stratify atypical hemolytic uremic syndrome long-term renal prognosis.