This paper deals with the issue of overall performance of combined transport terminals. It is important to take into account the "compatibility" and how it ties with other elements of the terminal so that the transition of the intermodal transport unit over individual elements of the combined transport terminal is as smooth as possible. Practical application of the methodology was verified in the Prerov combined transport terminal which lies on the main railway line number 330 Prerov Breclav, which is part of the second rail transit corridor in Czech Republic. The methodology consists of the optimization of all equipment and components performance in combined transport terminals comprising for example the handling equipment, reloading tracks, storage and reloading areas.