This paper discusses the design and implementation of certain project-based flexibility mechanisms introduced under the Kyoto Protocol. It argues that such mechanisms labour under three specific difficulties: a proliferation of operational forms, a multiplicity of underlying objectives, and the irreducible uncertainty arising from the counterfactual nature of the baseline. In the light of these difficulties, the authors set out an approach to the evaluation of joint implementation which has three main strands. Firstly, they investigate explicitly the impacts of baseline uncertainty on the emission reductions and costs associated with certain case study greenhouse gas abatement projects. Next, they set out the basis for an operational framework for flexibility in which streamlined procedures (baseline standardisation e.g.) are combined with institutional safeguards (baseline revision, limited crediting life, etc.). Finally, they suggest a methodology for evaluating each such framework in a given context, against the range of underlying objectives. The empirical results reported in this paper are based on a study of certain energy-sector case study projects implemented jointly between Northern and Eastern European countries. Nonetheless, the conceptual arguments developed here are relevant to all of the Kyoto flexibility mechanisms.