The Generalized Estimating Equations (GEE) approach is a widely used statistical method for analyzing longitudinal data and clustered data in clinical studies. In dentistry, due to multiple outcomes obtained from one patient, the outcomes produced from an individual patient are correlated with one another. This study focused on the basic ideas of GEE and introduced the types of covariance matrix and working correlation matrix. The quasi-likelihood information criterion (QIC) and quasi-likelihood information criterion approximation (QICu) were used to select the best working correlation matrix and the best fitting model for the correlated outcomes. The purpose of this study is to show a detailed process for the GEE analysis using SPSS software along with an orthodontic miniscrew example, and to help understand how to use GEE analysis in dental research.