Since multidrug-resistant gram-negative organisms have been increasing, polymyxin E (colistin) has been reintroduced despite its nephrotoxicity. A case-control study was performed to investigate the incidence, clinical characteristics and risk factors of colistin-induced nephrotoxicity. From August 2006 to June 2008, 47 cases receiving at least one defined daily dose (DDD) of intravenous colistin were included; 15 (31.9%) of the 47 cases developed nephrotoxicity with preserved urine output, 3 (20%) of whom underwent renal replacement therapy. The mean dosage of colistimethate sodium was 2.25 g (22.5 DDD; range 0.6-8.7 g) at the time of nephrotoxicity. Of 10 patients who were re-assessed for renal function after 1 month, 9 (90%) recovered their renal function. In the univariate analysis, site of infection, hypoalbuminaemia and cumulative dosage of the second-generation fluoroquinolones, aminoglycosides and non-steroidal anti-inflammatory drugs (NSAIDs) co-administered during colistin treatment as well as concomitant use of NSAIDs were risk factors for nephrotoxicity. However, in the logistic regression hypoalbuminaemia and the use of NSAIDs were significant risk factors for increased nephrotoxicity during colistin administration, suggesting that free colistin might cause renal toxicity. In conclusion, colistin-induced nephrotoxicity occurred at a high rate, and hypoalbuminaemia and concomitant use of NSAIDs were significant risk factors.