Abstract: A method for uncertainty evaluation of enrofloxacin and ciprofloxacin residues in chicken by high performance liquid chromatography (HPLC) was established.A mathematical model was constructed according to the basic method and procedure for uncertainty assessment given in JJF 1059-1999 Evaluation and Expression of Uncertainty in Measurement and CNAS-GL 06 Guidance on Evaluating the Uncertainty in Chemical Analysis.Each component of uncertainty in the whole measuring process was analyzed and quantified.Finally, the combined uncertainty and expanded uncertainty were achieved.The results showed that the major factors of uncertainty were standard curve fitting and sample pre-treatment.