This paper provides estimates of emissions of two important but often not well-characterized greenhouse gas (GHG) emissions related to transportation energy use: methane (CH₄) and nitrous oxide (N₂O). The paper focuses on emissions of CH₄ and N₂O from motor vehicles because unlike emissions of CO₂, which are relatively easy to estimate, emissions of CH₄ and N₂O are a function of many complex aspects of combustion dynamics and of the type of emission control systems used. They therefore cannot be derived easily and instead must be determined through the use of published emission factors for each combination of fuel, end-use technology, combustion conditions, and emission control system. Furthermore, emissions of CH₄ and N₂O may be particularly important with regard to the relative CO₂-equivalent GHG emissions of the use of alternative transportation fuels, in comparison with the use of conventional fuels. By analyzing a database of emission estimates, we develop emission factors for N₂O and CH₄ from conventional vehicles, in order to supplement recent EPA and IPCC estimates, and we estimate relative emissions of N₂O and CH₄ from different alternative fuel passenger cars, light-duty trucks, and heavy-duty vehicles.