Evidence from many clinical trials in recent years suggests that a large "treatment gap" exists between recommended therapies and the care that patients actually receive. This gap has been particularly apparent in the area of primary and secondary prevention of cardiovascular disease. In this article, three areas are discussed in which new scientific advances have not been adequately translated to clinical practice. These include: 1) the most appropriate measures to define the risks associated with obesity; 2) the under-diagnosis of obstructive sleep apnea and its relation to cardiovascular risk; and 3) the use and misuse of the exercise test and other functional status tools to predict health outcomes. Each is discussed in terms of how they should be quantified, their contribution to the estimation of cardiovascular disease risk, their response to interventions, and implications for cardiac rehabilitation. Clinical cardiac rehabilitation programs can benefit from routinely including these measures, both for their value in stratifying risk and for their importance in quantifying program efficacy. Physicians and allied health professionals should expand their routine medical evaluations and coronary risk factor profiling to include these measures.