Secondary peritonitis includes community-acquired and nosocomial peritonitis. These intra-abdominal infections have a common pathogenesis but some microbiological differences, particularly with respect to the type of bacteria recovered and the level of antimicrobial susceptibility. This report describes a prospective observational study of 93 consecutive patients with secondary peritonitis during an 11-month period. Community-acquired peritonitis accounted for 44 cases and nosocomial peritonitis for 49 cases (post-operative in 35 cases). Fifteen multidrug-resistant (MDR) bacteria were recovered from 14 patients. In univariate analysis, the presence of MDR bacteria was associated significantly with pre-operative and total hospital lengths of stay, previous use of antimicrobial therapy, and post-operative antimicrobial therapy duration and modifications. A 5-day cut-off in length of hospital stay had the best specificity (58%) and sensitivity (93%) for predicting whether MDR bacteria were present. In multivariate analysis, only a composite variable associating pre-operative hospital length of stay and previous use of antimicrobial therapy was a significant independent risk-factor for infection with MDR bacteria. In conclusion, knowledge of these two factors may provide a more rational basis for selecting initial antimicrobial therapy for patients with secondary peritonitis.