The aim of this study was to evaluate the prevalence and characteristics of carbapenemase-producing Enterobacteriaceae (CPE) from 3 tertiary-care Korean university hospitals between 2017 and 2018. Non-duplicated clinical isolates of Enterobacteriaceae showing resistance to any carbapenem agents were collected prospectively from 3 tertiary university hospitals between 2017 and 2018. The presence of carbapenemase genes was detected by multiplex PCR and sequencing for bla_KPC, bla_VIM, bla_NDM, bla_IMP, bla_OXA, and bla_GES was performed. Among the 690 potential carbapenem-resistant Enterobacteriaceae (CRE) isolates, 66.8% (N = 461) were CPE. The species distribution of CPE was as follows: Klebsiella pneumoniae was most common (75.9%), followed by Escherichia coli (15.0%), Citrobacter freundii (4.6%), Enterobacter cloacae (2.6%), Klebsiella. aerogenes (0.7%), and Klebsiella. oxytoca (0.4%). All 11 CPE genes were detected, particularly K. pneumoniae carbapenemase (KPC)-2 (87.6%), New Delhi metallo-β-lactamase (NDM)-1 (7.4%), NDM-5 (1.7%), KPC-3 (1.3%), oxacillinase (OXA)-232 (1.1%), and OXA-181 (1.1%). Six isolates produced 2 or 3 carbapenemases. The majority of the carbapenemase-producing C. freundii tested positive for NDM-1. We confirmed a high proportion of CPE among the CRE isolates with a high prevalence of KCP-2-producing K. pneumoniae and E. coli. Therefore, there is a need for undertaking continuous surveillance to monitor the prevalence of CPE.