The aim of this paper is to show the results obtained and the methodology used to achieve better logistic organization of Mediterranean ports and logistics areas. Recently, we introduced a new methodology in the ports of Naples and Algeciras Bay in order to improve their logistics processes. This methodology was implemented as a part of the INTE-TRANSIT project, cofinanced by the MED Program with the aim to improve logistic processes and increase technological integration in Mediterranean ports. The methodology used in the ports of Naples and Algeciras Bay consists of four parts, two of which include a tool called VSM. VSM stands for "Value Stream Mapping", a tool to analyze and understand the flow of material and information that allow a deep knowledge of a process and identify the wastes. "Waste" in this context, is defined as something anything that adds cost to a product or service without adding value. The use of this methodology has allowed us to identify in detail the problems in both the information flow and material flow. It was detected that the acquisition of new technologies could facilitate and expedite the process of receiving, the location, the internal movements and the vessel loading.