Loss of skeletal muscle in patients that have undergone gastric bypass is a consistent observation. Skeletal muscle constitutes the largest protein/amino acid pool in the body, and loss of skeletal muscle has important implications in health and disease. Sustaining a given level of muscle protein requires a balance between the rates of muscle protein synthesis and breakdown. Current evidence suggests that reduced rate of protein synthesis is implicated in the loss of muscle after gastric bypass. This is not surprising given a less than optimal dietary protein intake following the gastric bypass and because, unlike other macronutrients, protein/amino acids are not stored in the body. Ingesting essential amino acids, which cannot be synthesized de novo and have the primary role in the regulation of muscle protein synthesis, can potentially ameliorate loss of muscle protein after gastric bypass. At the same time, ingestion of essential amino acids provides a more efficient nutritional approach (i.e., greater stimulation of protein synthesis relative to the amount of amino acids ingested) to enhance muscle protein synthesis compared to the ingestion of intact protein in the gastric bypass patient. Changing current dietary practices towards increasing ingestion of essential amino acids provides an approach that can potentially prevent loss of lean body tissue and ultimately achieve a more sustained level of health in patients that have undergone gastric bypass.