Two different approaches to modeling the environmental fate of organic chemicals have been developed in recent years. The first approach is applied in multimedia box models, calculating average concentrations in homogeneous boxes which represent the different environmental media, based on intermedia partitioning, transport, and degradation processes. In the second approach, used in atmospheric transport models, the spatially and temporally variable atmospheric dynamics form the basis for calculating the environmental distribution of chemicals, from which also exchange processes to other environmental media are modeled. The main goal of the present study was to investigate if the multimedia mass balance models CliMoChem, SimpleBox, EVn-BETR, G-CIEMS, OECD Tool and the atmospheric transport models MSCE-POP and ADEPT predict the same rankings of the overall persistence (Pov) and long-range transport potential (LRTP) of POPs, and to explain differences and similarities between the rankings by the mass distributions and inter-compartment mass flows. The study was performed for a group of 14 reference chemicals. For Pov, the models yield consistent results, owing to the large influence of phase partitioning parameters and degradation rate constants, which are used similarly by all models. Concerning LRTP, there are larger differences between the models than for Pov, due to different LRTP calculation methods and spatial model resolutions. Between atmospheric transport models and multimedia fate models, no large differences in mass distributions and inter-compartment flows can be recognized. Deviations in mass flows are mainly caused by the geometrical design of the models.