Background: Patients negative for Shiga toxin-producing E. coli (STEC) are categorized as having atypical hemolytic uremic syndrome (HUS) and are associated with an increased risk for complement mutations and poorer prognosis compared with typical HUS. However, STEC identification is limited by the natural history of HUS. Methods: The current study is aimed at identifying HUS patients with poor outcomes based on the presence or absence of diarrhea (D) or Shiga toxin (S). A single-center retrospective review (2003–2012) of 42 HUS patients (follow-up 31.3 ± 38.7 months) was carried out. HUS was managed clinically with supportive treatments such as dialysis, plasma therapy, and eculizumab. Results: There was no significant difference in the D+S+ (31 %), D+S− (50 %) and D−S− (19 %) groups in the outcome variables of chronic kidney disease stages I–II (100 % vs 81 % vs 67 %) and proteinuria at follow-up (20 % vs 12.5 % vs 33.3 %), hospitalization duration (16.0 ± 8.7 vs 18.1 ± 9.5 vs 23.7 ± 12.9 days); dialysis requirement (50 % vs 81 % vs 66.7 %), and dialysis duration (10.2 ± 1.9 vs 33.3 ± 72.8 vs 10.3 ± 8.1 days). There was no significant difference in study outcomes in STEC+ (59 %) versus STEC– (41 %) groups. Genetic testing was performed in 12 % of HUS patients based on age, recurrent HUS, familial HUS, persistently low C3, or prolonged dialysis, and 80 % of the patients tested were positive for genetic mutations. Conclusions: Our study does not show poorer outcomes in STEC− HUS. Indications and the cost-effectiveness of genetic testing, eculizumab, and plasmapheresis in STEC− HUS need to be evaluated further.