Although the use of catheters in critically ill patients is mostly inevitable, this invasive procedure comes together with several health risks. Within this context, the contamination with Candida tropicalis is a primary concern as this highly prevalent pathogenic yeast can develop an extensive polymeric matrix that hinders the drugs' penetration and its effective treatment. This study addresses the potential for the 1-n-hexadecyl-3-methylimidazolium methanesulfonate (C16 MImMeS) and chloride (C16 MImCl) salts for eliminating the viable cells of biofilms of Candida tropicalis, compared to the performance of chlorhexidine (CHX) and fluconazole (FLZ). The minimum concentration required of C16 MImMeS, C16 MImCl, CHX and FLZ for elimination of the biofilm's viable cells (MBEC) was evaluated through microtitre plate biofilm exposure with different concentrations of these substances. These concentrations were determined at 80% of effective activity against the biofilm's viable cells by using the MTT reduction assay. C16 MImMeS and C16 MImCl were able to eliminate the viable cells at much lower concentrations (15·6 and 0·45 μg ml(-1) respectively) than CHX (1250 μg ml(-1) ) and FLZ (resistance of the viable cells). This demonstrates the high potential of these substances for nosocomial infections control. The 1-n-hexadecyl-3-methylimidazolium methanesulfonate (C16 MImMeS) and chloride (C16 MImCl) salts are extremely effective in eliminating the viable cells of Candida tropicalis biofilms, which allows the use of much lower concentrations than with the antimicrobial of choice (chlorhexidine) in hospital practices. These findings indicate these imidazolium salts as high-potential candidates for asepsis of medical environments and materials, including implants.