In both clinical and research settings, evaluation of the safety and efficacy of pharmacotherapy has traditionally relied upon changes in scale weight, ignoring measures of body composition changes, such as in body fat and fat-free mass (FFM). No FDA studies reported changes in body composition during the approval process for fenfluramine and dexfenfluramine, nor were any body composition studies reviewed in an article by the National Task Force on the Prevention and Treatment of Obesity on the safety and efficacy of long-term pharmacotherapy to manage obesity. Changes in scale weight can distort and obscure both positive and negative changes that occur in fat and FFM, which constitute an important screen for the safety and efficacy of a weight loss program. Furthermore, using loss of scale weight as the outcome criterion for weight loss programs can discourage the use of a behavior modification plan that affects scale weight losses through preservation of FFM. This study examined this potential source of bias and the extent to which integration of a behavior modification plan (which includes increased physical activity, improved dietary intake, and phytochemical glyconutritional dietary supplements) may improve the safety and efficacy of pharmacotherapy. Dual-energy x-ray absorptiometry measurements of body composition were performed in three groups of patients before and after a 60-day treatment period. Results of the study demonstrate that, although pharmacotherapy effected a significant reduction in scale weight, much of the loss was at the expense of FFM with no improvement in body composition. Conversely, the use of nutritional supplements and a behavior modification plan led to a preservation of FFM and significant improvement in body composition. In view of the widespread disregard of behavior modification programs in weight loss treatment plans that incorporate pharmacotherapy, these results offer another perspective on the success or failure of a weight loss program.