Central and Eastern Europe (CEE) is a rapidly changing and developing region which is making the transition to a market based economy. Along with economic reforms, the countries of the region are engaged in substantial environmental reforms, including climate change mitigation activities. Mitigation of, and adaptation to, the consequences of climate change are costly processes. It is therefore of great importance that the national and international mechanisms addressing these problems use methods both environmentally sound and economically efficient. Through two case studies that address the Clean Development Mechanism (CDM) in the Former Yugoslav Republic of Macedonia, and the Green Investment Scheme (GIS) in Romania, this paper explores challenges, related tasks and main problems in the establishment of mechanisms of the Kyoto Protocol in Central and Eastern Europe.