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Background US colorectal cancer screening guidelines for people at average risk for colorectal cancer endorse multiple screening options and recommend that screening decisions reflect individual patient preferences. Methods We used the Analytic Hierarchy Process (AHP) to ascertain decision priorities of people at average risk for colorectal cancer attending primary care practices in Rochester NY, Birmingham AL, and Indianapolis IN. The analysis included four decision criteria, three sub-criteria, and ten options. Results 484 people completed the study; 66% were female, 49% were African-American, 9% had low literacy skills, and 27% had low numeracy skills. Overall, preventing cancer was given the highest priority (mean priority 55%), followed by avoiding screening test side effects (mean priority 17%), minimizing false positive test results (mean priority 15%), and the combined priority of screening frequency, test preparation, and the test procedure(s) (mean priority 14%). Hierarchical cluster analysis revealed six distinct priority groupings containing multiple instances of decision priorities that differed from the average value by a factor of four or more. More than 90% of the study participants fully understood the concepts involved, 79% met AHP analysis quality standards, and 88% were willing to use similar methods to help make important healthcare decisions. Conclusion These results highlight the need to facilitate incorporation of patient preferences into colorectal cancer screening decisions. The large number of study participants able and willing to perform the complex AHP analysis used for this study suggests that the AHP is a useful tool for identifying the patient-specific priorities needed to ensure that screening decisions appropriately reflect individual patient preferences.