An investigation of fire and explosion hazards of different types of alternative fuel vehicles in tunnels is presented. The different fuels are divided into four types: liquid fuels, liquefied fuels, compressed gases, and electricity, and detailed parameters are obtained. Three types of fire hazards for the alternative fuel vehicles: pool fires, jet fires and fireballs are identified and investigated in detail. From the perspective of pool fire size, the liquid fuels pose equivalent or even much lower fire hazards compared to the traditionally used fuels, but the liquefied fuels may pose higher hazards. For pressurized tanks, the fires are generally much larger in size but shorter in duration. The gas releases from pressure relief devices and the resulting jet fires are highly transient. For hydrogen vehicles, the fire sizes are significantly higher compared to CNG tanks, while flame lengths only slighter longer. Investigation of the peak overpressure in case of an explosion in a tunnel was also carried out. The results showed that, for the vehicles investigated, the peak overpressure of tank rupture and BLEVE are mostly in a range of 0.1 to 0.36 bar at 50 m away. The situations in case of cloud explosion are mostly much more severe and intolerable. These hazards need to be carefully considered in both vehicle safety design and tunnel fire safety design. Further researches on these hazards are in urgent need.