Worldwide concerns about sulfur oxide (S[O.sub.x]) emissions from ships are motivating the replacement of marine residual oil (RO) with cleaner, lower-sulfur fuels, such as marine gas oil (MGO) and marine diesel oil (MDO). Vessel operators can use MGO and MDO directly or blended with RO to achieve environmental and economic objectives. Although expected to be much cleaner in terms of criteria pollutants, these fuels require additional energy in the upstream stages of the fuel cycle (i.e., fuel processing and refining), and thus raise questions about the net impacts on greenhouse gas emissions (primarily carbon dioxide [C[O.sub.2]]) because of production and use. This paper applies the Total Energy and Environmental Analysis for Marine Systems (TEAMS) model to conduct a total fuel cycle analysis of RO, MGO, MDO, and associated blends for a typical container ship. MGO and MDO blends achieve significant (70-85%) S[O.sub.x] emissions reductions compared with RO across a range of fuel quality and refining efficiency assumptions. We estimate C[O.sub.2] increases of less than 1% using best estimates of fuel quality and refinery efficiency parameters and demonstrate how these results vary based on parameter assumptions. Our analysis suggests that product refining efficiency influences the C[O.sub.2] tradeoff more than differences in the physical and energy parameters of the alternative fuels, suggesting that modest increases in C[O.sub.2] could be offset by efficiency improvements at some refineries. Our results help resolve conflicting estimates of greenhouse gas tradeoffs associated with fuel switching and other emissions control policies.