Background Eliciting patient preferences within the context of shared decision-making has been advocated for colorectal cancer (CRC) screening, yet providers often fail to comply with patient preferences that differ from their own. Purpose To determine whether risk stratification for advanced colorectal neoplasia (ACN) influences provider willingness to comply with patient preferences when selecting a desired CRC screening option. Design Randomized controlled trial Setting/Participants Asymptomatic, average risk patients due for CRC screening in an urban safety net healthcare setting. Intervention Patients were randomized 1:1 to a decision aid alone (n=168) or decision aid plus risk assessment (n= 173) arm between September 2012 and September 2014. Outcomes The primary outcome was concordance between patient preference and test ordered; secondary outcomes included patient satisfaction with the decision-making process, screening intentions, test completion rates and provider satisfaction. Results Although providers perceived risk stratification to be useful in selecting an appropriate screening test for their average-risk patients, no significant differences in concordance were observed between the decision aid alone and decision aid plus ACNI groups (88.1 vs. 85.0%, p=0.40) or high- and low-risk groups (84.5 vs. 87.1%, p=0.51). Concordance was highest for colonoscopy and relatively low for tests other than colonoscopy, regardless of study arm or risk group. Failure to comply with patient preferences was negatively associated with satisfaction with the decision-making process, screening intentions and test completion rates. Limitations Single institution setting; lack of provider education about the utility of risk stratification into their decision-making. Conclusions Providers perceived risk stratification to be useful in their decision-making but often failed to comply with patient preferences for tests other than colonoscopy, even among those deemed to be at low risk of ACN.