The application of panel analysis method in empirical sciences is increasing due to the numerous advantages it provides, such as greater efficiency of data, information and variability, which the commonly used methods of statistical analysis do not contain. Panel analysis is good in the social sciences for designing and testing more complex behavioral models, it can measure the dynamics of change and provide control over unobserved variables. Empirical research of regional supply chains of European Union countries is carried out in the paper with the help of econometric and statistical methods. The analysis was carried out on the number of observed units from 27 member states of the European Union in the time period from 2000 to 2019, using the method of random effects, first differences of fixed effects, the GMM method and quantile regression. In the research, quantile regression will prove to be adequate for the selected data set and will provide a better estimate compared to other models. It is concluded that the Croatian economy is dynamically well integrated into the regional supply chain of the European Union, which enables an increase in business competitiveness, efficiency and potential benefits for Croatia in the global organization of production.