Latvia takes an active part in research on the climate change issues and the country has undertaken EU and Kyoto obligations for CO2 emission reduction and increase of share of the renewable energy sources in energy supply mix. Dependence on imported energy sources, growth of electricity prices, the need for support to local producers are the main reasons for use of new renewable energy technologies in the Latvian energy sector. One of the technologies which are considered to take an important part in the future in Latvian energy sector is fuel cell cogeneration plants, which could play an important role not only in increase of use of domestically produced bio-ethanol, but also as the energy import minimizing solution with significance measurable in regional and global levels. Fuel cell technology is a rapidly developing technology in the world. Since the hydrogen, which is the fuel for most types of fuel cells, cannot be found on Earth in pure form, the ways of producing hydrogen from other energy sources are widely discussed. Liquid fuels can be stored easily in large quantities without losses and they are commercially available. Because of these qualities, liquid fuels are considered as one of the best hydrogen storage solutions for fuel cell systems. Ethanol, produced domestically from renewable feedstock is one of the most promising sources of hydrogen production for use in fuel cell cogeneration plants. The techno-economic model built with “RETScreen 4.0” simulation program (http://www.retscreen.net/) is presented in the work, and the model allows to evaluate the dependence of the main technical and economic parameters such as electricity production and primary savings relative to separate power and heat production, electricity production costs, achieved GHG emission reductions and financial viability of the bio-ethanol fuel cell cogeneration systems on various critical factors. The results obtained by the techno-economic model of bio-ethanol fuel cell cogeneration plant show the dependence of electricity production costs on bio-ethanol price, bio-ethanol reforming efficiency and investment costs. The electricity production costs of fuel cell cogeneration plant is compared with the electricity purchase tariff from cogeneration plants using renewable fuels set by the existing legislation. Data for hydrogen production from bio-ethanol via autothermal fuel processing is obtained for the model from previously made experimental investigation of small scale autothermal reforming reactor. The results show the technical and economic feasibility of bio-ethanol powered fuel cell cogeneration plants in Latvian energy supply system under several scenarios of development of critical impact factors.