The present report describes the use of MEKC in the presence of 35 mM sodium tetraborate, pH 9.0, containing 60 mM SDS for the complete separation and identification of creatinine, 1-methylhistidine (1-MeH) and 3-MeH in human urine. Their simultaneous quantification in urine of healthy controls and subjects submitted to elective surgery to their lower limbs allowed to use 3-MeH as a reliable measure of skeletal protein breakdown. Simplicity, sensitivity and low running costs are the main advantages of this method that is suitable for the routine analysis in clinical laboratories of a large number of samples per day.