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Estimates of the costs of medical care vary across patient populations, data sources, and methods. The objective of this study was to compare 3 approaches for estimating the incidence costs of colorectal cancer (CRC) care using similar patient populations, but different data sources and methods.We used 2 data sources, linked SEER-Medicare and Medicare claims alone, to identify newly diagnosed CRC patients aged 65 and older and estimated their healthcare costs during the observation period, 1998 to 2002. Controls were matched by sex, age-group, and geographic location. We compared mean net costs, measured as the difference in total cost between cases and controls, for: (1) a SEER-Medicare cohort, (2) a Medicare claims alone cohort, and (3) a modeled phase of care approach using linked SEER-Medicare data. The SEER-Medicare cohort approach was considered the reference.We found considerable variability across approaches for estimating net costs of care in CRC patients. In the first year after diagnosis, mean net costs were $32,648 (95% CI: $31,826 and $33,470) in the SEER-Medicare cohort. The other approaches understated mean net costs in year 1 by about 16%. Mean net 5-year costs of care were $37,227 (95% CI: $35,711 and $38,744) in the SEER-Medicare cohort, and $30,310 (95% CI: $25,894 and $34,726) in the claims only approach, with the largest difference in the 65 to 69 age group. Mean net 5-year costs of care were more similar to the reference in the modeled phase of care approach ($37,701 [range: $36,972 and $38,446]). Differences from the SEER-Medicare cohort estimates reflect misclassification of prevalent cancer patients as newly diagnosed patients in the Medicare claims only approach, and differences in years of data and assumptions about comparison groups in the modeled phase of care approach.CRC incidence cost estimates vary substantially depending on the strategy and data source for identifying newly diagnosed cancer patients and methods for estimating longitudinal costs. Our findings may inform estimation of costs for other cancers as well as other diseases.