In the framework of the Central European Study on Air pollution and Respiratory Health (CESAR), a risk perception and risk communication study was carried out in a total of 25 areas in Bulgaria, the Czech Republic, Hungary, Poland, Romania and the Slovak Republic. This paper is focused on the differences of perception between the Czech (CR) and the Slovak Republic (SR), and the other involved countries. The analysis is based on the data of a structured risk perception questionnaire survey of a random population sample. 6,043 completed questionnaires were collected from the total number of 14,400 distributed ones in 25 areas of the 6 countries. The risk perception was different in the CR and the SR, mainly concerning local environment and health of children in the CR and drug abuse including alcohol consumption and AIDS in the SR. In both countries environmental and health problems were seen as important, but the perceived responsibility for finding a solution was placed with different kinds of institutions.