For women with recurrent urinary tract infections (rUTI), the contribution of antibiotic use versus patient-related factors in determining the presence of antimicrobial resistance in faecal and urinary Escherichia coli, obtained from the same patient population, has not been assessed yet. Within the context of the 'Non-antibiotic prophylaxis for recurrent urinary tract infections' (NAPRUTI) study, the present study assessed determinants of antimicrobial resistance in E. coli isolated from urinary and faecal samples of women with rUTIs collected at baseline. Potential determinants of resistance were retrieved from self-administered questionnaires. From 434 asymptomatic women, 433 urinary and 424 faecal samples were obtained. E. coli was isolated from 146 (34%) urinary samples and from 336 (79%) faecal samples, and subsequently tested for antimicrobial susceptibility. Multivariable analysis showed trimethoprim/sulfamethoxazole (SXT) use three months prior to inclusion to be associated with urine E. coli resistance to amoxicillin (OR 3.6, 95% confidence interval: 1.3-9.9), amoxicillin-clavulanic acid (OR 4.4, 1.5-13.3), trimethoprim (OR 3.9, 1.4-10.5) and SXT (OR 3.2, 1.2-8.5), and with faecal E. coli resistance to trimethoprim (OR 2.0, 1.0-3.7). The number of UTIs in the preceding year was correlated with urine E. coli resistance to amoxicillin-clavulanic acid (OR 1.11, 1.01-1.22), trimethoprim (OR 1.13, 1.03-1.23) and SXT (OR 1.10, 1.01-1.19). Age was predictive for faecal E. coli resistance to amoxicillin (OR 1.02, 1.00-1.03), norfloxacin and ciprofloxacin (both OR 1.03, 1.01-1.06). In conclusion, in women with rUTI different determinants were found for urinary and faecal E. coli resistance. Previous antibiotic use and UTI history were associated with urine E. coli resistance and age was a predictor of faecal E. coli resistance. These associations could best be explained by cumulative antibiotic use.