Our primary objective was to assess the screening preferences of patients at familial risk of colorectal cancer. Asymptomatic subjects aged 18–75 with a single first-degree relative diagnosed with colorectal cancer (n = 48) or polyps (n = 52) were asked to identify a preferred screening strategy, test features influencing their choice, and level of interest in decision-making after reviewing a decision aid describing the pros and cons of currently recommended screening tests. Although both groups preferred colonoscopy, 40% of subjects with a family history of colorectal cancer and 48% of those with a family history of polyps preferred alternative strategies. Accuracy was the most commonly identified test feature influencing test preference. Most subjects (66%) felt that selection of screening test should be a patient dominant or shared process. We conclude that patients at familial risk of colorectal cancer have distinct screening preferences that often vary from current recommendations.