Alternative fuels research has been on going for well over many years at a number of institutions. Driven by oil price and consumption, engine emissions and climate change, along with the lack of sustainable fossil fuels, transportation sector has generated an interest in alternative, renewable sources of fuel for internal combustion engines. The focus has ranged from feed stock optimization to engine-out emissions, performance and durability. Biofuels for transportation sector, including alcohols (ethanol, methanol.etc.), biodiesel, and other liquid and gaseous fuels such as methane and hydrogen, have the potential to displace a considerable amount of petroleum-based fuels around the world. First generation biofuels are produced from sugars, starches, or vegetable oils. On the contrary, the second generation biofuels are produced from cellulosic materials, agricultural wastes, switch grasses and algae rather than sugar and starch. By not using food crops, second generation biofuel production is much more sustainable and has a lower impact on food production. Also known as advanced biofuels, the second-generation biofuels are still in the development stage. Combining higher energy yields, lower requirements for fertilizer and land, and the absence of competition with food, second generation biofuels, when available at prices equivalent to petroleum derived products, offer a truly sustainable alternative for transportation fuels. There are main four issues related to alternative fuels: production, transportation, storage, handling and usage. This paper presents a review of recent literature related to the alternative fuels usage and the impact of these fuels on fuel injection systems, and fuel atomization and sprays for both spark-ignition and compression-ignition engines. Effect of these renewable fuels on both internal flow and external flow characteristics of the fuel injector will be presented.