Abstract: Guanidination plays an obvious role in identification and quantification of proteins. A quick microwaveassisted guanidination reaction method was established in this work. The reaction conditions， including buffer pH, concentration of O-methylisourea hemisulfate and time of microwave heating， were optimized using a standard peptide. The peptide was microwave heated for 1 min with 1.5 mol/L O-methylisourea and near pH 12 of the mixture, the conversion rate of lysine to homoarginine was 99%.Further examination was carried out by applying this microwave-assisted guanidination method to tryptic digested peptides of myoglobin and bovine albumin. The average guanidination efficiency was higher than that reported in literature. Compared with the conventional guanidination methods, the microwave-assisted guanidination method can shorten reaction time, enhance reaction efficiency, and reduce side reactions on the N-terminal of peptides.