This paper describes a model, which simulates the cotton biomass supply chain. The research has been carried out within the frame of a project that examined the feasibility of producing energy from the chopped cotton-plant stalks after they are cut and after the seed cotton is collected. The heating value of the dry stalks, is high and can be used for the production of combined heat and power (CHP co-generation). Thessally is the biggest cotton harvesting area of Greece and Europe. The study focuses on this area where the cotton-stalks are not used for energy production yet. There have not been any studies focusing on the specifications of this renewable source of energy and on the specifications of its harvesting area. This study examines the feasibility and the problems that arise while trying to organize an integrated logistics network and optimize its transportation economy. Also, economic aspects of other logistics procedures like collection and warehousing, are analysed.