Measurement of urinary 3-methylhistidine (3MH) excretion is the primary in vivo method to measure skeletal muscle (myofibrillar) protein breakdown. This method requires quantitative collection of urine and is based on the assumption that no metabolism of 3MH occurs once it is released from actin and myosin. This is true in most species, but in sheep and swine a proportion is retained in muscle as a dipeptide, balenine. In neither of these species does urine 3MH yield any data on the metabolism of 3MH. We have conducted studies that propose that 3MH metabolism in humans, cattle, dogs, swine, and sheep can be defined from a single bolus infusion of a stable isotope 3-[methyl-2H3]-methylhistidine. Following the bolus dose of the stable isotope tracer, serial blood samples and/or urine was collected over three to five days. A minimum of three exponentials were required to describe the plasma decay curve adequately. The kinetic linear-time-invariant models of 3MH metabolism in the whole animal were constructed by using the SAAM/CONSAM modeling program. Three different configurations of a three-compartment model are described: (A) A simple three-compartment model for humans, cattle, and dogs, in which plasma kinetics (3-[methyl-2H3]-MH/3MH) are described by compartment 1 and with one urinary exit from compartment 1. (B) A plasma-urinary kinetic three-compartment model with two exits was used for sheep with a urinary exit out of compartment 1 and a balenine exit out of a tissue compartment 3. (C) A plasma three-compartment model was used in swine with an exit out of a tissue compartment 3. The kinetic parameters reflect the differences in known physiology of humans, cattle, and dogs as compared to sheep and swine that do not quantitatively excrete 3MH into the urine. Steady-state model calculations define masses and fluxes of 3MH between three compartments and, importantly, the de novo production of 3MH. The de novo production of 3MH for humans, cattle, dogs, sheep, and swine are 3.1, 6.0, 12.1, 10.3, and 7.2 mumol x kg-1 x d-1, respectively. The de novo production of 3MH as calculated by the compartmental model was not different when compared to 3MH production as calculated via traditional urinary collection. Additionally, data suggest that steady-state compartment masses and mass transfer rates may be related to fat free mass and muscle mass in humans and swine, respectively. In conclusion, models of 3MH metabolism have been developed in numerous species, and these models can be used for the assessment of muscle proteolysis and 3MH kinetics without the collection of urine. This methodology is less evasive and will be useful in testing further experimental designs that alter myofibrillar protein breakdown.