In the article the issues of establishing and functioning of the zones with special economic activity conditions are addressed and their impact on the environment in Russia and Kazakhstan is assessed. The relevance of the subject of the research is determined, on the one hand, by a qualitative change in the role of the environmental issues in the system of values of population of the post-soviet countries and, on the other hand, by cumulative increase of the negative impact due to the irrational environmental management. Information about the types of special status zones established in these countries is systematized. The key characteristics of these institutional entities are compared, which includes goals and specifics of their development, implemented organizational mechanisms, measures for support of business activities, offered tax incentives and preferences. The authors demonstrate that the adopted accelerated economic growth strategy within the framework of zones with special status is implemented disregarding the environmental effects of their development, which poses serious threats to self-preservation of the society and environment. Common and country-specific risks of functioning of the zones with special economic activity conditions are justified. Factors contributing to inadequate assessment of the negative impact on the environment of industries, created in SEZ were revealed. It is emphasized that the current legal and regulatory framework of these zones in Russia and Kazakhstan is aimed not at the prevention of environmental threats but at the easing of requirements for entities in the field of environmental management. Finally, conclusion is made about the greening opportunities of development of the zones with special economic activity conditions, a necessity to enhance the environmental legislation and mutual “best practices” adoption opportunities in this field in Russia and Kazakhstan. The empirical basis of the analysis is constituted by the results of the studies carried out within the framework of the research work “Enhancement of the State Regulation Policy of Accelerated Clustering of the Industrial Regions” implemented on the grounds of the grant funding of the Ministry of Education and Science of the Republic of Kazakhstan.