The study was undertaken to characterize the time course of biochemical parameters in skeletal muscle during critical illness to gain information for the design of a suitable protocol for interventional studies using metabolic or nutritional manipulation. Critically ill patients in our intensive care unit ([ICU] N = 9) were investigated on two separate sampling occasions with percutaneous muscle biopsies for determination of protein, nucleic acids, free amino acids, energy-rich phosphates, fat, water, and electrolytes. The first biopsy specimen was taken 3 to 11 days after admission and the second biopsy specimen 3 to 7 days later. Protein concentration, expressed as alkali-soluble protein (ASP)/DNA, decreased by 12% (P <.02) between the two biopsies. The total free amino acid content was only 50% of normal, but remained unaltered over time. In particular, the concentration of glutamine remained low, approximately 25% of normal, In contrast, branched chain amino acid (BCAA) increased by 25% (P <.05) and phenylalanine by 55% (P <.05) between biopsies. The fat content related to fat-free solid (FFS) increased by 130% (P <.001) between the two biopsies. Muscle water did not change during the study period, The extracellular portion was double the normal value when related to FFS. Intracellular water, on the other hand, was outside the 95% confidence interval for normal values in the second biopsy. The concentrations of adenosine triphosphate (ATP), creatine, phosphocreatine, and the phosphorylated fraction of total creatine remained at the same level between the two biopsies. We conclude that in critically ill patients, there is a decrease in protein content over time and increases in BCAA, phenylalanine, and fat content, while the low glutamine level and high extracellular water content remain unaltered. The temporal alterations were well characterized after a 5-day study period. Copyright (C) 1997 by W.B. Saunders Company.