The article focuses on the issue of evaluation of economic sustainability of transportation and shipping companies. The economic crisis, which is currently abating in many world’s countries, has affected all industries, including transportation and shipping. This important sector of national economy with a multifunctional character has been influenced by the economic recession very significantly and its consequences are visible even now. For this reason there is a growing demand for methods allowing comprehensive evaluation of businesses. This article contributes to the topic by describing a procedure for development of a model for comprehensive evaluation of transportation and shipping companies. The model makes it possible to monitor, to evaluate and to signal financial health and performance of such companies. Finally, the model is validated and its predictive power is assessed. The proposed model is an output from research conducted by the Institute of Technology and Business in České Budějovice, Czech Republic.