Background: In Crohn’s disease (CD), intra-abdominal abscess (IA) and intestinal free-wall perforation (IP) have a common mechanism of transmural inflammation; however, their manifestation is different. Objective: This study aimed to investigate differences in the clinical features between IA and IP in Korean patients with Crohn’s disease. Design: A retrospective cohort study. Setting: Thirty university hospitals and two local hospitals in Korea. Patients: Patients who were diagnosed with CD between July 1982 and December 2008 were enrolled. Main Outcome Measures: Clinical characteristics of IA and IP. Results: Among 1286 patients with CD, 147 (11.4%) had IA and 83 (6.5%) had IP. IA patients were younger than those of IP (24.2 ± 8.6 vs. 30.4 ± 11.1 years, p = 0.001). Location and behavior were significantly different between IA and IP (p = 0.035 and 0.021). In multivariate analyses, perianal fistula was not associated with increased risk of IA and IP, while intestinal stricture was associated with increased risk of IA (OR: 2.72, p < 0.0001) and IP (OR: 2.76, p < 0.0001). In subgroup analyses, 55 (36.5%) IA patients were diagnosed at the diagnosis of CD, and 92 (63.5%) during follow-up of CD, while 47 (56.6%) IP patients were diagnosed at the diagnosis of CD, and 36 (43.3%) during follow-up of CD. Conclusions: There are several differences in the clinical features of IA and IP in Korean patients with CD. The development mechanism is considered as identical, but further investigation should be needed for clinical implication.