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Retrospective studies have identified elevated vancomycin trough levels >20 mg/L as a predictor of nephrotoxicity with a high variable incidence of 12.6%–65%. However, the elevated levels may represent the effect of renal compromise rather than the cause of nephrotoxicity. The aim of this study was to report the incidence of acute kidney injury (AKI) and associated risk factors in adult patients with vancomycin trough levels >20 mg/L in a prospective Pharmacovigilance Program from Laboratory Signals at a Hospital.This was a prospective follow-up of all cases with serum vancomycin trough levels >20 mg/L between June 2010 and May 2011. AKI was defined using the Risk, Injury, Failure, Loss, End-stage criteria. Patients with vancomycin-induced AKI (VIAKI) were compared with vancomycin-tolerant patients.During 12 months of study, 271 samples corresponding to 179 cases were monitored. Vancomycin did not alter the renal function in 68.2% [95% confidence interval (CI): 60.8–74.9] of cases, and 13.4% (95% CI: 8.8–19.3) of AKI cases were induced by other causes. Nephrotoxicity without AKI criteria was found in 10.1% (95% CI: 6.1–15.4) of cases, and VIAKI occurred in 8.4% (95% CI: 4.8–13.4) of cases. The VIAKI group had a significantly lower basal glomerular filtration rate at baseline and higher vancomycin trough levels at the time of the signal. The majority of the group was in the intensive care unit and received nephrotoxic agents during vancomycin therapy. The most frequent stage of VIAKI was injury (53.3%). VIAKI occurred after 7 days (range: 3–14) of treatment, and in 53.3% of cases, the daily dose was >30 mg/kg. Renal function was recovered at discharge in 73.3% of cases and 66.7% of cases had other suspected drugs.The Pharmacovigilance Program from Laboratory Signals at a Hospital provides early identification and early evaluation of cases. Renal function and vancomycin trough levels should be closely monitored from the second week of treatment in adults, intensive care patients, and those who receive concurrent nephrotoxic agents.