Objective:To explore the application of the generalized estimating equation (GEE)in the repeated measures data.Method:The repeated measures data were analyzed with category variance outcome by GEE and conclusions were drawn according to the estimating of parameter and standard error.Results:The method could efficiently consider the intra-class correlation,advisably deal with the missing value,correctly obtain the estimate and standard error of the each effect,by applying GEE in repeated measures data.Conclusion:It can gain more objective appraise of medication effect by the application of the GEE in the repeated measures data,and to deserve to be generalized.