In this study, the causative bacteria and their sensitivity to various antimicrobial agents as well as risk factors for quinolone-resistant Escherichia coli were investigated in patients with acute uncomplicated cystitis or complicated cystitis by isolation and culture of bacteria from urine samples. In total, 1312 strains were isolated from 1009 patients with acute uncomplicated cystitis, including E. coli (63.3%), Enterococcus faecalis (12.8%) and Streptococcus agalactiae (4.6%). In addition, 994 strains were isolated from 725 patients with complicated cystitis, including E. coli (36.4%), E. faecalis (19.2%), Klebsiella pneumoniae (5.0%), S. agalactiae (4.7%) and Pseudomonas aeruginosa (4.5%). At least 90% of E. coli isolates from acute uncomplicated cystitis showed sensitivity to fluoroquinolones and cephems, whilst 70.4-88.4% of E. coli isolates from complicated cystitis were sensitive to fluoroquinolones and 85.4-89.5% were sensitive to cephems. Factors associated with quinolone-resistant E. coli included two or more episodes of cystitis within 1 year, failure of quinolone therapy, underlying urinary tract disease, prior quinolone treatment within 1 month and age ≥75 years. It is important to confirm the sensitivity of causative bacteria for optimal antimicrobial therapy, and empirical antimicrobial agents should be selected by considering patient characteristics and other factors.