Carbon emission
Despite emitting less carbon than fossil fuels, it cannot be ignored that the nature of biofuels is that it does emit carbon. If we are to invest heavily in renewable technologies aimed at reducing our carbon emissions, we should perhaps consider this fact very carefully before developing our investment in biofuels too heavily.
Food or Fuel?
Land taken up by biofuel crops is land that isn't being used for food crops. With cost of living rising in line with food shortages in various parts of the world, increasing biofuel production is likely to make the problem worse.
Land use
One of the factors influencing climate change is land use. To aid growth of crops, many farmers (unless using organic farming methods) use fertilizers. If synthetic, these often decay into various nitrogen products, which can be powerful greenhouse agents.
Also, vast fields of similarly coloured land can affect the albedo (reflectivity) of the land, and reflect less energy back into space.
Long "Life Cycle"
Imagine a wind turbine. The wind blows, electricity powers your house, your car, or goes back into the grid. Brilliant. Not so with biofuels, however: the crop takes many months to grow, it must be treated to convert it into a form we can use, it must be distributed to vehicles (or perhaps a biofuel power plant, one day?) and then burnt.
The are many more steps which increase costs, pollutants and energy requirements (in transport and machinery).
Return to alternative energy sources from disadvantages of biofuels