The prevalence of extended-spectrum β-lactamase (ESBL) in Enterobacteriaceae has been increasing worldwide. The aims of this study were to determine the prevalence of ESBLs among clinical isolates of Escherichia coli obtained from 2000 to 2010 in Japan, and to characterize the sequence type (ST) and antimicrobial susceptibility of the bla(CTX-M)-carrying strains. The genes for β-lactamases were determined by conventional PCR and sequencing, and the antimicrobial susceptibility test was performed by the broth microdilution method. Among the 948 strains, 35 were judged as ESBL-positive strains. The positive rates ranged from 0.6% to 3.9% until 2008, but surged to 10.3% in 2010. Thirty-three of them carried bla(CTX-M), but all were negative for ESBL-type bla(TEM) and bla(SHV). bla(CTX-M-14) was the most prevalent (18/33) among bla(CTX-M)-carrying strains, followed by bla(CTX-M-15) (7/33) of which five were isolated in 2008 and 2010. Additionally, bla(CTX-M-27) appeared in 2010 for the first time in this study and accounted for more than a third of the bla(CTX-M)-carrying strains. From the MLST analysis, ST131 known as a world pandemic clone, has been predominantly isolated since 2006. The major types of ESBLs carried by ST131 strains clearly shifted from bla(CTX-M-14) to bla(CTX-M-15) and/or bla(CTX-M-27) between 2006 and 2010. Most of these isolates were still susceptible to doripenem, latamoxef (moxalactam), flomoxef and cefmetazole. Our results suggest that a change of the dominant type of ESBL among Enterobacteriaceae is currently in progress in Japan, and therefore further periodic surveillance is needed.