Abstract A variety of diet approaches achieve moderate weight loss in many individuals. Yet, most diet interventions fail to achieve meaningful weight loss in more than a few individuals, likely due to inadequate adherence to the diet. It is widely conjectured that targeting the diet to an individual's food preferences will enhance adherence, thereby improving weight loss. This article describes the design considerations of a study protocol aimed at testing this hypothesis. The study is a 2-arm randomized trial recruiting 216 medical outpatients with BMI ≥ 30 kg/m2 followed for 48 weeks. Participants in the experimental arm (Choice) select from two of the most widely studied diets for weight loss, a low-carbohydrate, calorie-unrestricted diet (LCD) or a low-fat, reduced-calorie diet (LFD). The participant's choice is informed by results from a validated food preference questionnaire and a discussion of diet options with trained personnel. Choice participants are given the option to switch to the other diet after three months, if desired. Participants in the Control arm are randomly assigned to follow one of the two diets for the duration of follow-up. The primary outcome is weight assessed every 2–4 weeks for 48 weeks. Secondary outcomes include adherence to diet by food frequency questionnaire and obesity-specific health-related quality of life. If assisting patients to choose their diet enhances adherence and increases weight loss, the results will support the provision of diet options to patients who desire weight loss, and bring us one step closer to remediating the obesity epidemic faced by our healthcare systems.