BACKGROUND: Ciprofloxacin is the antibiotic most frequently used in the treatment of Crohn's disease (CD). We attempted to identify the microorganisms present in CD-related intra-abdominal abscesses, their ciprofloxacin resistance patterns, and the clinical impact. METHODS: Microorganisms, their ciprofloxacin resistance, and clinical outcomes were retrospectively analyzed in 78 CD patients with intra-abdominal abscesses, who underwent percutaneous drainage between March 1991, and November 2011. RESULTS: The median time from diagnosis of CD to abscess drainage was 59.5 months (range, 1 to 178 mo). As for bacteriology, the no-growth proportion was 38.5% (n=30), and 69 microorganisms belonging to 11 genera were isolated from the other 48 (61.5%) patients. Of the 69 microorganisms, 65 were bacteria, including 30 (43.4%) gram-positive, 28 (40.6%) gram-negative aerobes, 7 (10.1%) gram-negative anaerobes, and 4 (4.1%) fungi. Streptococci spp. (25, 36.2%) were the most common bacteria, followed by Escherichia coli (18, 26.1%). Nineteen of the 28 gram-negative aerobes (67.9%) were resistant to ciprofloxacin, including 14 of 18 (77.8%) E. coli isolates. When we compared clinical characteristics and treatment outcomes in 17 patients with ciprofloxacin-resistant and 8 with ciprofloxacin-sensitive bacteria, we found that disease duration from diagnosis to drainage (97.2 vs. 50.7 mo, P=0.03) and median length of hospitalization (40 vs. 31 d, P=0.03) was significantly longer in the former. CONCLUSIONS: When gram-negative aerobes were isolated from abscesses in CD patients, more than two thirds were resistant to ciprofloxacin. Providers should consider this high rate of ciprofloxacin resistance when choosing first-line antibiotic treatment for CD-related intra-abdominal abscesses.