Like fossil fuels, biofuels produce carbon dioxide. But unlike fossil fuels, the carbon dioxide produced comes from plants that sucked it out of the air last year, rather than millions of years ago. This means that biofuels are a form of closed-end recycling, whereby the waste product goes directly into production of the fuel.
Pollution is any byproduct that cannot be fed back into the closed-end ==system. For biofuels, this includes particulates and unburnt hydrocarbons (smoke), oxides of nitrogen, carbon monoxide, and a few others. These are typically much lower level than when fossil fuel is combusted, but they remain a problem.
What is pollution for one technology may be the biofuel in another. For example, if wood is heated anaerobically (with limited oxygen), it produces carbon monoxide, which is normally considered a pollutant, but if collected, can be burnt as a biofuel.
Further negative aspects:
With the increased emphasis being placed on bio-fuels by some governments, including EU regulations which rule that, in future, bio-fuels should replace a set percentage of fossil fuels, there is worry that more and more land could be taken away from food production and put into production of crops for bio-fuel production. This is the Food versus Fuel debate. In addition, there is the worry that further areas of rain forest, e.g. in Brazil, could be de-forested in order to plant crops such as sugar-cane for bio-fuel (ethanol) production. Both of these negative aspects are likely to have an impact on the inhabitants and small farmers of poorer “third world” countries rather than on North American or European populations.
Small scale bio-fuel use, such as wood-burning central heating systems for co-housing projects and intentional communities, can be ecologically sensible. Large scale bio-fuel use, such as the production and sale by the multi-national fuel companies of vegetable oils and ethanol to fuel motor transport does not significantly solve the problem of too many cars and trucks producing too much pollution.