A direct comparison among highly uncertain inventories of emissions is inadequate and may lead to paradoxes. This issue is of particular importance in the case of greenhouse gases. This paper reviews the methods for the comparison of uncertain inventories in the context of compliance checking. The problem is treated as a comparison of uncertain alternatives. It provides a categorization and ranking of the inventories which can induce compliance checking conditions. Two groups of techniques to compare uncertain estimates are considered in the paper: probabilistic and fuzzy approaches. They show certain similarities which are revealed and stressed throughout the paper. The group of methods most suitable for the compliance purpose is distinguished. They introduce new conditions for fulfilling compliance, depending on inventory uncertainty. These new conditions considerably change the present approach, where only the reported values of inventories are accounted for.