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In this paper we demonstrate that the institutional arrangement (or: design) of Joint Implementation (JI) and the Clean Development Mechanism (CDM) has a decisive impact on their cost-effectiveness. We illustrate our arguments by statistically analyzing the costs from 94 Activities Implemented Jointly (AIJ) pilot phase projects as well as by adjusting these data on the basis of simple mathematical formulas. These calculations explicitly take into account the institutional differences between JI (sinks, no banking) and the CDM (banking, no sinks) under the Kyoto Protocol and also show the possible effects on credit costs of alternative design options. However, our numerical illustrations should be viewed with caution, because AIJ is only to a limited extent representative of potential future JI and CDM projects and because credit costs are not credit prices. Some of the main figures found in this study are: an average cost figure per unit of emission reduction for AIJ projects of 46 dollar per ton of carbon dioxide equivalent ($/Mg CO2-eq), an average potential JI credit cost figure which is lowered to 37 $/Mg CO2-eq by introducing banking and an average of 6 $/Mg CO2-eq per credit for potential low-cost CDM projects which includes sinks. However, at CoP6 in November 2000 in The Hague (The Netherlands), the Parties to the Framework Convention on Climate Change (FCCC) did not (yet) reach consensus on the institutional details of the project-based mechanisms, such as the possible arrangement of early JI action or the inclusion of sinks under the CDM.