This paper presents results concerning fire and explosion hazards of various alternative fuel vehicles in tunnels. The alternative fuels are divided into four types: liquid fuels, liquefied fuels, compressed gases, and electricity, and detailed parameters are obtained. Three important types of fire hazards: pool fires, jet fires and fireballs are identified and investigated. From the perspective of pool fire size, the liquid fuels pose equivalent or even lower fire hazards compared to traditionally used fuels, but the hazards of liquefied fuels may be higher. For pressurized tanks, fires are generally much larger in size but shorter in duration. The gas releases from pressure relief devices and the resulting jet flames are highly transient. For hydrogen vehicles, the fire sizes are significantly higher compared to CNG tanks, while flame lengths are only slighter longer. Analysis of the peak overpressure in case of an explosion in a tunnel shows that the consequences of tank rupture and BLEVE are relatively tolerable for a position further than 100 m away, but the situations in case of a cloud explosion are highly severe and intolerable for tunnel users in most cases. These hazards need to be carefully considered in both vehicle safety design and tunnel fire safety design.