Biomass is a renewable and cheap resource for biofuel production. Yet, the viability and feasibility of biofuel production from agricultural biomass depends upon its availability at a competitive cost. The present study investigates the Greek biomass potential for bioethanol and biodiesel production, as well as the energy potential of agricultural residues using a GIS-based management application built on a relational database system. The computations were based on geographical and time-depending data provided by the National Statistical Service of Greece, while the digital maps of land cover overlaid provides by Marathon Data Systems. Typical input data included cultivation areas sorted by geographical region, agricultural production of the crops, by-product factors, availability factors, and energy factors, for the period 2000-2010. The output included the productivity of the main crops in the corresponding areas, as well as their by-products and available energy. The study concludes with a discussion on the significance and the challenges of biomass supply, including brief descriptions about economical, social, environmental and technical aspects of biofuel production.