Abstract: AIM　To establish a standard method of peptide mapping analysis for quality control of rhIL-11. METHODS　To find out the best tryptic digestion and chromatogram conditions by using Alliance HPLC system and automatic temperature-controlled injector. RESULTS　Peptide mappings of three continuous batches of samples rhIL-11 are completely identical. Comparing with that of reference rhIL-11, 20 of the 21 peaks are all the same, but the area and height of the sixth peak are smaller than those of the reference product. Moreover, there is one extra peak between the ninth and tenth peak. It is stated that there are minor differences between the protein structure of the samples and that of the reference. The sixth and extra peaks of digested mixture of samples were separated and collected. Determination of amino acid sequence of two collected fragments indicates that there are two extra amino acids at the N-terminal of the sample, which leads to the detail differences. CONCLUSION　The method has high degree of accuracy, automation and fine duplication, which can be applied for quality control of rhIL-11.