Breakthroughs in genetic testing have informed patients and physicians in the treatment of breast cancer; however, they have also added to the complexity of decision-making. Genetic testing for breast cancer susceptibility not only changes treatment and screening options, but also challenges the way in which interventions are evaluated. While comparative effectiveness and cost-effective analysis methods are now standard for evaluation at the societal level, technologies such as genetic testing require us to consider the role of patient preference, especially as we move towards more personalized approaches to medicine. In this review, we discuss the changing role of pharmacoeconomics and outcomes research by highlighting how the discipline could use patient preference methods, such as conjoint analysis, to promote shared decision-making and to empower breast cancer patients. By adopting these methods we could move our focus from what is best for payers or society to one that applies scientific methods to identify what is best for patients.