For a variety of reasons, significant differences and uncertainties surround specific quantitative estimates of mitigation costs. Cost estimates differ because of the (a) methodology used in the analysis, and (b) underlying factors and assumptions built into the analysis. Bottom-up models incorporate detailed studies of engineering costs of a wide range of available and anticipated technologies, and describe energy consumption in great detail. However, they typically incorporate relatively little detail on non-energy consumer behavior and interactions with other sectors of the economy. The costs estimated by bottom-up models can range from negative values (due to the adoption of "no-regrets" options) to positive values. Negative costs indicate that the direct energy benefits of a mitigation option exceed its direct costs (net capital, operating, and maintenance costs). Market and institutional barriers, however, can prevent, delay, or make more costly the adoption of these options. Inclusion of implementation and policy costs would add to the costs estimated by bottom-up models.

Top-down models are aggregate models of the economy that often draw on analysis of historical trends and relationships to predict the large-scale interactions between sectors of the economy, especially the interactions between the energy sector and the rest of the economy. Top-down models typically incorporate relatively little detail on energy consumption and technological change. The costs estimated by top-down models usually range from zero to positive values. This is because negative cost options estimated in bottom-up models are assumed to be adopted in both the baseline and policy scenarios. This is an important factor in the differences in the estimates from these two types of models.

The inclusion of some factors will lead to lower cost estimates and others to higher estimates. Incorporating multiple greenhouse gases, sinks, induced technical change, and emissions trading can lower costs. Further, studies suggest that some sources of greenhouse gas emissions can be limited at no or negative net social cost to the extent that policies can exploit no-regret opportunities such as correcting market imperfections, inclusion of ancillary benefits, and efficient tax revenue recycling. International cooperation that facilitates cost-effective emissions reductions can lower mitigation costs. On the other hand, accounting for potential short-term macro shocks to the economy, constraints on the use of domestic and international market mechanisms, high transaction costs, inclusion of ancillary costs, and ineffective tax recycling measures can increase estimated costs. Since no analysis incorporates all relevant factors affecting mitigation costs, estimated costs may not reflect the actual costs of implementing mitigation actions.