Colonoscopy procedure is effective in colorectal cancer surveillance. An understanding of variations in the cost or charge for this procedure would aid in designing economic evaluations of colorectal cancer screening and prevention strategies. OBJECTIVE: To examine charges related to colonoscopy and differences therein based on type of colonoscopy and malignancy status. METHODS: Data were from the PharMetrics Outcomes Database, an aggregated administrative database of 35 managed care plans. Colonoscopy procedures (N=4,055) between January 1 to June 30, 1997 were identified. The CPT codes were used to identify the type of colonoscopy (with or without polypectomy) and the ICD-9 codes were used to determine diagnostic outcomes (malignant, benign, or no tumor) of colonoscopy. Charges associated with the visit and colonoscopy procedure were identified and differences determined using the ANOVA or t-test approach. RESULTS: Fifty-five percent of patients were females and 77% were greater than 50 years old. A majority (83%) of benign neoplasm patients had colonoscopy with polypectomy vs. 57% for malignant neoplasm patients. The overall mean charges for a colonoscopy visit was $2,536, of which colonoscopy procedure charge was $1,146. The mean charges for colonoscopy procedure accompanied by polypectomy was $1,245 and colonoscopy without polypectomy was $971 (p<0.05). A similar trend was observed with the total colonoscopy visit charges. Statistically significant differences (p<0.05) in mean colonoscopy procedure charges between benign ($1,208) versus no neoplasm ($1,000), benign versus malignant ($1,100), and malignant versus no neoplasm groups were observed. CONCLUSION: Differences in colonoscopy-related charges based on type and malignancy status need to be accounted for in the economic evaluation of colorectal cancer screening and prevention strategies.