Distinguishing true coagulase-negative staphylococci bacteremia from contamination remains a challenge. We conducted a retrospective analysis of 183 patients with methicillin-resistant coagulase-negative staphylococci (MR-CoNS)-positive and methicillin-resistant Staphylococcus aureus-positive cultures obtained from sterile sites such as blood, synovial fluid, ascitic fluid, and cerebrospinal fluid. Of the 209 MR-CoNS isolates, 83 (39.7%) were considered infection associated, and 126 (60.3%) were considered contamination. MR-CoNS isolates cultured from synovial fluid were more likely to be infection associated (P = 0.009). The median interval from insertion of a central venous catheter to onset of infection tended to be longer in MR-CoNS infection cases than in methicillin-resistant S. aureus infection cases (41 days versus 14 days, P = 0.055). In conclusion, our results suggest that the proportion of cases of true MR-CoNS infection may be higher than previously reported.