Genetically modified organisms cannot be regarded as merely a topic for academic debate, since these have serious implications as a research field and for production based on genetic engineering. Public debates rarely base their arguments on elements rooted in scientific arguments and knowledge but are heavily loaded with emotions, opinions and informal reasoning. This study aimed to investigate the knowledge and acceptance of genetically modified organisms among prospective teachers in Slovenia and Turkey. Knowledge of genetic modification was measured with a two-tier instrument. The level of acceptance of genetic modification was measured with a 17-item instrument. Findings revealed that knowledge of genetics and biotechnology barely influenced the acceptability of genetic modification, and correlations are low. The relationship between knowledge and acceptance was not significant among Slovenian students and while significant for the Turkish or combined groups, the r values were only 0.179 and 0.244. It was found that differences in the acceptability of clusters of different kinds of genetically modified organisms do exist between the two countries. In both countries, participants recognized microorganisms and plants that produce something useful as the most acceptable organisms, while at the other end were animals used for consumption or as donors of organs. Practical implications for teaching are discussed and implications for further studies are drawn.