BACKGROUND: A standardized treatment for gastrointestinal stromal tumors (GIST) of the colon and rectum has not been clearly established. The objective of this study is to examine our experience in patients with colorectal GISTs and review the appropriate surgical management. METHODS: The medical records of patients with colorectal GIST treated in our institution between 1995 and 2005 were reviewed. The malignant potential of the GIST was assessed with the current consensus criteria defined by the National Institutes of Health. Clinical parameters were also evaluated to determine prognostic factors. RESULTS: There were 10 male and 7 female patients, with a median age of 64 years (range: 19 - 84). Bloody stool and abdominal pain were the most commonly reported symptoms in colorectal GISTs. There were 7 colonic GISTs and 10 rectal GISTs. Sixteen patients underwent surgery with a margin of negative resection including 12 radical surgical resections, 3 transanal wide excisions, and one colonoscopic excision. Pathological results revealed a high risk in 8 patients (47.1 %), an intermediate risk in 4 (23.5 %), a low risk in 3 (17.6 %), and a very low risk in 2 (11.8 %). Three patients (3 / 16, 18.6 %) developed disease relapse after primary radical resection. All the three patients were high-risk rectal GISTs, accounting for 42.9 % (3 / 7) in the high-risk group. The median time to disease relapse was 15.7 months (range: 6 - 24). Cox regression analysis showed that variables including age, gender, and tumor size were not presenting statistically significant differences between groups of relapse and non-relapse patients. CONCLUSION: Non-high-risk colorectal GISTs bear a good prognosis after margin-negative surgery. Transanal wide excision for non-high-risk GISTs is mandatory if a complete resection can be performed. Abdominoperineal resection would be preserved only in patients with high risk or large non-high-risk lower rectal GISTs. The high-risk group has high incidence of relapse even though a complete resection was achieved. Adjuvant therapy with a tyrosine kinase inhibitor would be beneficial to these patients.