There were presented key directions of innovative activity that led to the emergence of biotechnological solutions and the creation of second and third generation biofuels. There was characterized the complex of basic economic risks which it is necessary to consider at the organization of manufacture and use of biofuel. Based on the results of analysis, new opportunities in the conversion of industrial and agricultural waste, including organic, containing lignocelluloses biomass, A number of conditions and prerequisites for the establishment of industrialized production complexes in the Russian Federation that can transform organic waste into biofuel. It is noted that the background allows us to consider the development of biofuel production in Russia as a promising innovative path for various areas of economic activity that positively affects the state of the environment.