Research into the role of diet in health faces a number of methodologic challenges in the choice of study design, measurement methods, and analytic options. Heavier reliance on randomized controlled trial (RCT) designs is suggested as a way to solve these challenges. We present and discuss 7 inherent and practical considerations with special relevance to RCTs designed to study diet: 1) the need for narrow focus; 2) the choice of subjects and exposures; 3) blinding of the intervention; 4) perceived asymmetry of treatment in relation to need; 5) temporal relations between dietary exposures and putative outcomes; 6) strict adherence to the intervention protocol, despite potential clinical counter-indications; and 7) the need to maintain methodologic rigor, including measuring diet carefully and frequently. Alternatives, including observational studies and adaptive intervention designs, are presented and discussed. Given high noise-to-signal ratios interjected by using inaccurate assessment methods in studies with weak or inappropriate study designs (including RCTs), it is conceivable and indeed likely that effects of diet are underestimated. No matter which designs are used, studies will require continued improvement in the assessment of dietary intake. As technology continues to improve, there is potential for enhanced accuracy and reduced user burden of dietary assessments that are applicable to a wide variety of study designs, including RCTs.