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.