Background Urinary tract infections (UTIs) are frequently caused by Enterococcus spp. We aim to define the risk factors involved in UTIs caused by Enterococcus. Determine the overall mortality and predictive risk factors. Methods A retrospective in-patients study was conducted with bacteriemic UTIs caused by Enterococcus spp. We compared bacteriemic UTIs caused by Enterococcus spp. vs. a random sample of 100 in-patients with bacteriemic UTIs caused by others enterobacteria. Results We found 106 in-patients with UTIs caused by Enterococcus spp., 51 of whom had concomitant positive blood cultures. Distribution by species was: 83% E. faecalis and 17% E. faecium, with a Charlson comorbidity index of 5.9 ± 2.9. When we compared bacteriemic UTIs caused by Enterococcus spp. vs. bacteriemic UTIs caused by others enterobacteria we found the following independent predictors of bacteriemic UTI by Enterococcus: male sex with an OR of 6.1 (95%CI 2.3–16.1), uropathy with an OR of 4.1 (1.6–10.1), nosocomial infection with an OR of 3.8 (1.4–10.3), urinary cancer with an OR of 6.4 (1.3–30.3) and previous antimicrobial treatment with an OR of 18 (5.2–62.1). Overall, in-patient mortality was 16.5%, which was associated with a higher Sequential Organ Failure Assessment (SOFA) score (> 4), severe comorbidity such as immunosuppression, malignant hemopathy and nephrostomy, or Enterococcus faecium species and its pattern or resistance to ampicillin or vancomycin (p < 0.05). Appropriate empiric antibiotic therapy was not associated with a better prognosis (p > 0.05). Conclusions Enterococcus spp. is a frequent cause of complicated UTI by a profile of risk factors. High mortality secondary to a severe clinical setting and high comorbidity may be sufficient reasons for implementing empiric treatment of patients at risk, although we did not show a higher survival rate in patients with this treatment strategy.