Although numerous epidemiologic and lipid intervention studies clearly demonstrate the pivotal role of high-density lipoprotein cholesterol (HDL-C) on risk of coronary artery disease (CAD), the National Cholesterol Education Program (NCEP) has emphasized only total cholesterol and low-density lipoprotein cholesterol (LDL-C), and has underemphasized the role of HDL-C in their lipid assessment and treatment recommendations. In a review of 113 consecutive patients in our cardiac rehabilitation program, lipid levels improved modestly with cardiac rehabilitation. "Ideal" lipids (LDL-C < 130 mg/dL according to the NCEP) were present in 49% before the rehabilitation program and in 46% afterward. In fact, 60 (53%) of our patients had total cholesterol levels < 200 mg/dL and would require no further lipid assessment or treatment according to the NCEP. Of these 60 patients, 40 (67%) had low HDL-C (< or = 35 mg/dL). In our total study group, 56% (63/113) had HDL-C < or = 35 mg/dL and 33% (37/113) had HDL-C < or = 30 mg/dL before rehabilitation (compared to 42% and 21%, respectively, after rehabilitation. On the other hand, a "high-risk" LDL-C value (> or = 160 mg/dL) was found in only 17% of patients at baseline and in only 13% after the cardiac rehabilitation program. Using an approach that incorporates the pivotal role of both LDL-C and HDL-C (LDL-C > or = 160 mg/dL or HDL-C < or = 35 mg/dL) for our patients with known CAD, 65% would require drug treatment before rehabilitation and 53% after rehabilitation. We conclude that: (1) lipids improve only modestly (though the change is significant statistically) with cardiac rehabilitation; (2) low levels of HDL-C are prevalent in cardiac rehabilitation patients and are much more prevalent than elevated LDL-C, both before and after rehabilitation; and (3) the NCEP should reevaluate the pivotal role of HDL-C in its assessment and treatment guidelines, particularly in patients with known CAD, since emphasis on both LDL-C and HDL-C is needed for optimal primary and secondary prevention of CAD.